Will I only have to change the config files shown in order to keep my servers world or am I going to have to change the config on all 95 mods?.
Just do it. Do it now, do it quickly. I would much rather lose my progress now than get a few weeks down the line and lose that much more when it hits the point that there's no option but to do a full fix due to something like a new mod being added.
is it possible to throw a band aid on there while doing a full fix? Since a full fix could possibly take a while.