debian mark and unmark non free repositories

You'll need to remove the non-free software installed.

vrms would be useful for that purpose.
https://packages.debian.org/jessie/vrms

To my limited understanding, a repo is nothing but a server.
Unmarking it should only remove access to it, not to what you installed from it.

vrms is the tool for the job in Debian. It goes through all your packages and checks where they came from; if they came from a "contrib", "non-free", "restricted", or "multiverse" section, it lists them appropriately.

From the "Synaptic Pacage Manager" (in the "System Settings"), click the "Origin" button in the bottom-left part of the window, then choose the non-free section above, select all the listed of packages (a click on the first one and a shift click on the last one), right-click on the selection, choose "Mark for Complete Removal", click on the "Apply" button and confirm.