I'd be very surprised if Calibre
formally tracks the content of a book's 'data' subfolder
via its database.
I make extensive use of the 'data' subfolder feature, have done since the day (literally) it was released. And because it didn't exist at that time, I do not use the Manage data file feature… still don't.
I manage the content of the 'data' folders using: Windows File Explorer, zabkat's xplorer˛, LopeSoft's FileMenu Tools, and AHK scripts.
And, afaik there can only be
one subfolder in a calibre book folder, and it
must be named 'data', anything else will generate this error in Check Library…
unless it's in the Names/Extensions to ignore.
BR