Some files exist in the target, but are not shown by 'ls' nor 'dir'

[ephestione]

Source folder is a dropbox subfolder, contains a php web application running on a local webserver. It contains upwards of 24000 files, and almost 3000 folders.
It has been used for years on windows with EncFSMP, only today I realized that some files (including index.php itself), even if correctly served by XAMPP, just do not show in file manager.
I wouldn't know when the problem actually started to occur, but it obviously hasn't always been like this.
They are not hidden files, and anyway filemanager is set to show hidden files.
I have identified some of these files because I wanted to edit them but they are not "findable".
Anyway, if on the commandline I do "dir filename" and "type filename" the results are as expected. Just, when I do "dir" they are not shown together with the other files.
If, in File Manager, I try to create a file with that same filename, filemanager asks if instead I want to create "filename (2)".

I also tested with encfs4win by jetwhiz under windows, and by mounting the same source folder with encfs under a virtualboxed ubuntu server distro. Under linux, I cannot see them with "ls", but they are shown if I do "ls filename".

This doesn't appear to interfere with the normal operation of the local website, as all the files are accessible to XAMPP's Apache when specifically requested, but it is obviously a blocking issue when I want to edit the files, as I cannot see them in Netbeans, and especially if I want to make backup copies with either robocopy under windows or rsync (cwrsync) because they effectively do not show, and thus are not copied rendering the backup incomplete.

Also, I know some files that are surely "missing" because I went and looked for them, but I wouldn't know how many and which other files have the same problem.

Alas, this is the only copy that I have, or rather, the encrypted copy is the only hardcopy, I have no other useable/complete clear copies...

Also, EncFSMP typically shows the "ERROR Invalid data size, not multiple of block size" repeating many many times in its log window, together with a time and a three digit numerical id.

[ephestione]

Actually, while File Manager stats for the source folder are as stated above, the stats for the mounted target folder are worringly smaller: upwards of 22000 files, and little more than 2700 folders... and here I'm getting the creeps, as the data inside has been collected in years and it would be a huge hit to lose it even partially