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I'm not sure how it will work, but if you're worried, just move the download folder before you remove it from within the application. Better yet, if you have the space, just copy the folder somewhere else.
Hopefully someone else has a better answer for you.
This is one of the reasons docker is so great. If you were running the application in docker, you would have mounted that folder as a volume, so if you wanted to move it you'd just stop the container, move the folder, edit your compose file to point to the new location, restart, and from the application's point of view nothing will have changed.
Just what I want to do, move files from A to B in an easy 8 step process!
I kid, I kid...
Docker is wonderful when it is used for the right purposes.