One possibility is that you at some time recently moved the calibre library or renamed it. Afterwards you experienced problems and added all the books in the library to the library again. Then you could end up with duplicates in the calibre library. One book that calibre knows about, and one that calibre has lost their track of.
The library maintenance functions should be able to fix the problem.
If you moved the calibre library so the path became a little longer, then the files would have to be more truncated now, just as you describe.
I seem to recall an update some time ago when the length of the paths/filenames were updated. Shortened. If it was long ago since you updated calibre that might have something to do with it as well. But it shouldn't cause any problem, except when trying to rebuild the calibre library. Then the new filenames/paths would be shorter.
To avoid this problem avoid having the calibre library at a place with a long path. Preferably just use the C:\mybooks or something like that, like theducks suggests.
I don't use Windows so I don't experience this problem and I am not sure how you can best avoid the his problem in the future. The safest way to move the calibre library from one Windows computer to another could be to use exactly the same paths on both computers. If that isn't possible, make sure that the new path is shorter. If you need to use a longer path, use the GUI and copy the books from one library to another.
Another way to avoid problems with Windows and limitations for the paths is that you could start using Linux to run calibre. Perhaps in a VM. VirtualBox is nice, and free.
