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Using Jamroom
upload the /modules directory over top of whatever is there now.
When jamroom updates via the marketplace it takes whatever is at
/modules/jrCore
and moves it to
/modules/jrCore-version-6.?.?
Then adds a symlink to point to that location.
If you upload the /modules you will overwrite the symlink with a new folder which will be symlinked to again when you update via the ACP marketplace system.
All your data is in the database and safe.