Not enough information.
Do you use the "download" feature of the FMS admin console?
Do you open the files locally after downloading from the server --> if so, there is no suprise there: the local path to the FMS data is diffferent than the one when the file is hosted.
No I ran a backup for the file before finding it in the folder, then after finding it I compressed it and dragged it to my desktop. I am using RemoteDesktop while doing this. I then opened the new file on the server after closing and removing the previous version.
Still lost on your exact procedurre. What exactly do you do? Explain step by step.
You say that you run a backup on FMS but then find the backup file in Finder and drag it to your desktop. What you do select, just the FM file? If you replace just that FM file with a new copy then of course it will not know the links to the Remote Container data files, because they were not used in that file to begin with...