System Re-install question

Does anyone know if I re-install my system if it will delete all hidden files? or re-write over them?

It's possible that the external drive is now mounting on the wrong path because a "ghost" folder of the same name was created in the /Volumes directory of your startup drive when the external drive went offline. If this happened, then the system might now be unable to mount the real external drive without changing the name of the mount point, usually by adding a number. This would change the path to your files, and any pointers to their previous paths would now be wrong.
Using Finder, navigate to one of the graphic files on your external drive, right-click it and Get Info, and look at General>Where at the top. If the name of your external volume is, say, "Graphics", the path you see should begin with:
/Volumes/Graphics/..
Does the volume name instead have an added number, something like:
/Volumes/Graphics 1 /...
If so, then you probably do have a "ghost folder' in /Volumes.
I would take a look there in any event. /Volumes is a hidden folder, but it is easy to peek into it. First *eject and then disconnect all external drives*, then:
Finder>Go menu> Go to Folder
enter /Volumes and click Go
/Volumes should contain what looks like an alias to the startup volume. Don't touch that, or any other alias. Do you also see a folder which is not an alias, with a name similar to your (currently disconnected) external drive? If so, look inside it to be sure it does not contain any of your actual graphics files. If it doesn't, trash the folder, but for safety, don't empty the Trash yet. Reboot, and then reconnect your external drive.

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