[BUGFIX] sys_file record doesn't get flagged as delete

File is deleted by driver and deleted property of FileObject is set by
ResourceStorage but new state is not persisted.

Update deleted property in updateProperties array in FileObject and
persist change.

Fixes: #48336
Releases: 6.2, 6.1, 6.0
Change-Id: I6cac106dcf89125e0b98b8b12a03c0b3f56d484f
Reviewed-on: https://review.typo3.org/20982
Reviewed-by: Steffen Ritter
Tested-by: Steffen Ritter