I added audits for "/var/lib/apt/lists/" and it looks like "packagekit" is clearing the apt repo metadata. This happened during user login.
I didn't do much analysis, and the logs could be completely normal (not sure?) # ausearch -k apt_lists_delete_bug -i <some output> .. ---- type=PROCTITLE msg=audit(04/10/26 07:35:37.930:210020) : proctitle=/usr/libexec/packagekitd type=PATH msg=audit(04/10/26 07:35:37.930:210020) : item=1 name=deb.debian.org_debian_dists_unstable_contrib_dep11_icons-64x64.tar.gz inode=1832111 dev=08:03 mode=file,644 ouid=root ogid=root rdev=00:00 nametype=DELETE cap_fp=none cap_fi=none cap_fe=0 cap_fver=0 cap_frootid=0 type=PATH msg=audit(04/10/26 07:35:37.930:210020) : item=0 name=/ inode=1831457 dev=08:03 mode=dir,755 ouid=root ogid=root rdev=00:00 nametype=PARENT cap_fp=none cap_fi=none cap_fe=0 cap_fver=0 cap_frootid=0 type=CWD msg=audit(04/10/26 07:35:37.930:210020) : cwd=/ type=SYSCALL msg=audit(04/10/26 07:35:37.930:210020) : arch=x86_64 syscall=unlinkat success=yes exit=0 a0=0xd a1=0x7f3e58029210 a2=0x0 a3=0x7f3e6d4beaa0 items=2 ppid=1 pid=313068 auid=unset uid=root gid=root euid=root suid=root fsuid=root egid=root sgid=root fsgid=root tty=(none) ses=unset comm=PK-Backend exe=/usr/libexec/packagekitd subj=unconfined key=apt_lists_delete_bug ---- type=PROCTITLE msg=audit(04/10/26 07:35:37.930:210021) : proctitle=/usr/libexec/packagekitd type=PATH msg=audit(04/10/26 07:35:37.930:210021) : item=1 name=packages.element.io_debian_dists_default_main_binary-amd64_Packages inode=1839446 dev=08:03 mode=file,644 ouid=root ogid=root rdev=00:00 nametype=DELETE cap_fp=none cap_fi=none cap_fe=0 cap_fver=0 cap_frootid=0 type=PATH msg=audit(04/10/26 07:35:37.930:210021) : item=0 name=/ inode=1831457 dev=08:03 mode=dir,755 ouid=root ogid=root rdev=00:00 nametype=PARENT cap_fp=none cap_fi=none cap_fe=0 cap_fver=0 cap_frootid=0 type=CWD msg=audit(04/10/26 07:35:37.930:210021) : cwd=/ type=SYSCALL msg=audit(04/10/26 07:35:37.930:210021) : arch=x86_64 syscall=unlinkat success=yes exit=0 a0=0xd a1=0x7f3e58029210 a2=0x0 a3=0x7f3e6d4beaa0 items=2 ppid=1 pid=313068 auid=unset uid=root gid=root euid=root suid=root fsuid=root egid=root sgid=root fsgid=root tty=(none) ses=unset comm=PK-Backend exe=/usr/libexec/packagekitd subj=unconfined key=apt_lists_delete_bug ---- type=PROCTITLE msg=audit(04/10/26 07:35:37.930:210022) : proctitle=/usr/libexec/packagekitd type=PATH msg=audit(04/10/26 07:35:37.930:210022) : item=1 name=deb.debian.org_debian_dists_unstable_non-free_source_Sources inode=1833821 dev=08:03 mode=file,644 ouid=root ogid=root rdev=00:00 nametype=DELETE cap_fp=none cap_fi=none cap_fe=0 cap_fver=0 cap_frootid=0 type=PATH msg=audit(04/10/26 07:35:37.930:210022) : item=0 name=/ inode=1831457 dev=08:03 mode=dir,755 ouid=root ogid=root rdev=00:00 nametype=PARENT cap_fp=none cap_fi=none cap_fe=0 cap_fver=0 cap_frootid=0 type=CWD msg=audit(04/10/26 07:35:37.930:210022) : cwd=/ type=SYSCALL msg=audit(04/10/26 07:35:37.930:210022) : arch=x86_64 syscall=unlinkat success=yes exit=0 a0=0xd a1=0x7f3e58029210 a2=0x0 a3=0x7f3e6d4beaa0 items=2 ppid=1 pid=313068 auid=unset uid=root gid=root euid=root suid=root fsuid=root egid=root sgid=root fsgid=root tty=(none) ses=unset comm=PK-Backend exe=/usr/libexec/packagekitd subj=unconfined key=apt_lists_delete_bug ---- .. <more output> Logs from packagekit (1.4.0-1) and gnome-software (51.0-1) around the same time. Oct 04 07:34:56 mstar PackageKit[313068]: daemon start Oct 04 07:35:26 mstar gnome-software[314767]: gs_icon_downloader_update_priority: assertion 'GS_IS_ICON_DOWNLOADER (self)' failed Oct 04 07:35:34 mstar PackageKit[313068]: uid 1001 is trying to obtain org.freedesktop.packagekit.system-sources-refresh auth (only_trusted:0) Oct 04 07:35:34 mstar PackageKit[313068]: uid 1001 obtained auth for org.freedesktop.packagekit.system-sources-refresh Oct 04 07:35:38 mstar PackageKit[313068]: refresh-cache transaction /38197_bdceaaaa from uid 1001 finished with cancelled-priority after 3044ms Oct 04 07:35:38 mstar gnome-software[314767]: internal error: failed, but no error code: cancelled-priority Oct 04 07:35:38 mstar PackageKit[313068]: resolve transaction /38198_bbeeadab from uid 1001 finished with success after 227ms Oct 04 07:35:38 mstar gnome-software[314767]: Only 0 apps for curated list, hiding Oct 04 07:35:44 mstar gnome-software[314767]: updates-shell: failed to get upgrades: no plugin could handle listing distro upgrades Oct 04 07:35:44 mstar PackageKit[313068]: get-updates transaction /38199_cbaecadc from uid 1001 finished with success after 174ms Oct 04 07:35:46 mstar PackageKit[313068]: search-file transaction /38200_edbaaecc from uid 1001 finished with success after 1329ms Oct 04 07:35:46 mstar PackageKit[313068]: search-file transaction /38201_bbbeddde from uid 1001 finished with success after 257ms Oct 04 07:35:46 mstar PackageKit[313068]: search-file transaction /38202_daddedab from uid 1001 finished with success after 255ms Oct 04 07:35:46 mstar PackageKit[313068]: search-file transaction /38203_bedcbdcb from uid 1001 finished with success after 257ms Oct 04 07:35:47 mstar PackageKit[313068]: search-file transaction /38204_eaaaddbc from uid 1001 finished with success after 257ms Oct 04 07:35:47 mstar PackageKit[313068]: search-file transaction /38205_bedeccbb from uid 1001 finished with success after 258ms Oct 04 07:35:47 mstar PackageKit[313068]: search-file transaction /38206_dadbebeb from uid 1001 finished with success after 257ms Oct 04 07:35:47 mstar PackageKit[313068]: search-file transaction /38207_bcaeaeca from uid 1001 finished with success after 259ms Oct 04 07:35:48 mstar PackageKit[313068]: search-file transaction /38208_eecccdad from uid 1001 finished with success after 256ms Oct 04 07:35:48 mstar PackageKit[313068]: search-file transaction /38209_eaccadad from uid 1001 finished with success after 260ms Oct 04 07:35:48 mstar PackageKit[313068]: search-file transaction /38210_eedaeabb from uid 1001 finished with success after 264ms Oct 04 07:35:48 mstar PackageKit[313068]: search-file transaction /38211_aaacaeea from uid 1001 finished with success after 256ms Oct 04 07:35:49 mstar PackageKit[313068]: search-file transaction /38212_bbaabdba from uid 1001 finished with success after 261ms Oct 04 07:35:49 mstar PackageKit[313068]: search-file transaction /38213_dbacdcba from uid 1001 finished with success after 256ms Oct 04 07:35:49 mstar PackageKit[313068]: search-file transaction /38214_acebcddc from uid 1001 finished with success after 258ms Oct 04 07:35:50 mstar PackageKit[313068]: search-file transaction /38215_deebbaeb from uid 1001 finished with success after 256ms Oct 04 07:35:50 mstar PackageKit[313068]: search-file transaction /38216_ceaaddcb from uid 1001 finished with success after 256ms Oct 04 07:35:50 mstar PackageKit[313068]: search-file transaction /38217_cebaaccb from uid 1001 finished with success after 257ms Oct 04 07:35:50 mstar PackageKit[313068]: search-file transaction /38218_edebdbbe from uid 1001 finished with success after 254ms Oct 04 07:35:51 mstar PackageKit[313068]: search-file transaction /38219_deddeddb from uid 1001 finished with success after 265ms Oct 04 07:35:51 mstar PackageKit[313068]: search-file transaction /38220_ccbebbda from uid 1001 finished with success after 259ms Oct 04 07:35:51 mstar PackageKit[313068]: search-file transaction /38221_bdbadecb from uid 1001 finished with success after 258ms Oct 04 07:35:51 mstar PackageKit[313068]: search-file transaction /38222_deedabaa from uid 1001 finished with success after 266ms Oct 04 07:35:52 mstar PackageKit[313068]: search-file transaction /38223_ccbacaae from uid 1001 finished with success after 263ms Oct 04 07:35:52 mstar PackageKit[313068]: search-file transaction /38224_ddcbccca from uid 1001 finished with success after 267ms Oct 04 07:35:52 mstar PackageKit[313068]: get-updates transaction /38225_dcdcbace from uid 1001 finished with success after 141ms Oct 04 07:36:35 mstar gnome-software[314767]: failed to get upgrades: no plugin could handle listing distro upgrades Oct 04 07:36:35 mstar PackageKit[313068]: uid 1001 is trying to obtain org.freedesktop.packagekit.system-sources-refresh auth (only_trusted:0) Oct 04 07:36:35 mstar PackageKit[313068]: uid 1001 obtained auth for org.freedesktop.packagekit.system-sources-refresh Oct 04 07:36:42 mstar PackageKit[313068]: refresh-cache transaction /38226_ddbbcada from uid 1001 finished with failed after 7136ms Oct 04 07:36:42 mstar PackageKit[313068]: get-updates transaction /38227_beaecbee from uid 1001 finished with success after 195ms Oct 04 07:41:47 mstar PackageKit[313068]: daemon quit
