Inspect the contents, not just the filename
Jellyfin 10.11 introduced pattern handling for non-empty .ignore files. Older installations treated their contents differently. A marker containing a human note can therefore need review even when its name has not changed.
Classify the intended rule
For each existing marker, write whether the goal is to exclude the entire directory or only selected items. Keep a copy of the earlier file. If the whole directory should remain excluded, follow the current empty-marker rule and store explanatory notes somewhere else.
Do not empty every marker indiscriminately. A file that intentionally contains patterns on a current server has a different purpose. Check version, content and expected scope together, especially when a directory is shared between more than one maintained installation.
Recheck a boundary sample
After the appropriate rescan, verify both one excluded item and one nearby item that should stay visible. Record the result against the version being deployed. This makes an upgrade review specific enough to detect accidental exposure or overbroad hiding without deleting or moving the original media.
Questions answered
Can a comment-only marker safely mean exclude everything?
Do not assume that on current releases. Use the documented empty-marker behaviour when that is the intended scope.
Should I remove every non-empty marker during an upgrade?
No. Review whether it is legacy content or an intentional current pattern list.
Sources & further reading
Official references for the subjects discussed. Service terms and device software can change.