We are using variable 7.x-2.5.
It seems that the structure of form state values when saving variables has changed. This causes files to not be updated to a permanent status.

CommentFileSizeAuthor
#2 variable_extra-file_managed_save_permanent-2696711-1.patch1006 bytesDerimagia
variable_extra-form_state_values.patch843 bytesbceyssens
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bceyssens created an issue. See original summary.

Derimagia’s picture

Derimagia CreditAttribution: Derimagia as a volunteer commented
Status: Active » Reviewed & tested by the community
FileSize
variable_extra-file_managed_save_permanent-2696711-1.patch1006 bytes

Attached is a more valid patch (paths were wrong)

Derimagia’s picture

Derimagia CreditAttribution: Derimagia as a volunteer commented
Status: Reviewed & tested by the community » Needs work

Actually this needs more work. I believe this only fixes it on some of the variable pages and breaks it on others.