Dear Vincent, thank you for your report.
Please check whether atopacctd is still running? You are upgrading from version 2.24 which had a bug in atopacctd that left it hanging around and only killable by SIGKILL. The message "/run/pacct_shadow.d: File exists" hints at a still running atopacctd. This has been an upstream issue, which is fixed in atop 2.25 I think. I upgraded from atop 2.25 to 2.26 without any issue. Since for Jessie => Stretch the upgrade will be between 1.26-2 and 2.26, I do not expect this issue to happen. Additionally I do not agree with the severity of grave for this bug report. The package is definately usable. However I leave it to Marc, the maintainer of the atop package, to downgrade the severity to what he sees fits. Thanks, -- Martin