I suspect that "apt-daily-upgrade.service" and "apt-daily.service" (both call 
/usr/lib/apt/apt.systemd.daily) cause Synaptic to rebuild apt-xapian-index. I 
disabled them with 
sudo systemctl disable apt-daily.timer
sudo systemctl disable apt-daily-upgrade.timer

I'm not on production server, so I think I can do so. Do not repeat this
if unsure.

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https://bugs.launchpad.net/bugs/1685376

Title:
  Synaptic rebuilds search index very often and inefficient

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