Uploading the file outside of the Admin panel process may be failing to set permissions properly for the server, something the admin panel upload does for you behind the scenes. That could keep it from appearing as accessible to the server panel.
If the backup folder was changed, it is also possible that permissions on any or all of the other server directories may have been affected, possibly stopping your access via the admin panel.
As your IT person to check and reset the permissions on the server directories as outlined in the documentation. It might be best to stop FM Server while that is being done.
Stehen has the right and left of it,
You should always close the DB when touching permissions. FMS checks permissions on opening the file so if you change them midstream FMS won't know about it. And if you make a mistake and switch it from R/W to RO then FMS may close without saving the file the next time it tries to write to it.
Here's another one. This may help also.
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