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^What NiLuJe said. It's quite likely that the file ended up getting a new identifier when you modified it. And because the experts at lab126 seem to never have heard about database normalization or referential integrity, it seems quite likely that you ended up with an inconsistent collections database after overwriting the file.
Could you either post here, or -- probably preferrable for privacy reasons -- send me via PM, your collections database (/var/local/cc.db) ? I'd like to take a look at it and see what kind of inconsistencies there are.
Alternatively, you can also do that yourself - the file is a plain SQLite database. The format isn't too hard to understand.
Your best bet to (hopefully) fix this is to export the collections to calibre via CM, then manually delete the /var/local/cc.db, restart the device, import from calibre via CM. And in the future, to prevent this from happening again: make any needed adjustments to files before you start filing them into collections.
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