[BUGFIX] Deleted flag is not updated during file indexing

If sys_file records (file objects) have set the deleted flag, it
won't be removed once the file is physically available again
with the same file name (identifier).

Change-Id: Id6dc7466764ac3994606204edadc9c2a7d2106c8
Fixes: #50525
Releases: 6.0, 6.1, 6.2
Reviewed-on: https://review.typo3.org/22695
Reviewed-by: Oliver Hader
Tested-by: Oliver Hader