Well, to start, yeah uninstalling the mods with JSGME before installing the next patch is widely agreed to be a good plan. Plus it's easy as pie with that program. Just make sure if you have a ton of stuff in your mod folder to export to a txt file the mods you have running before the uninstall of everything. Might save you a small headache later.
Secondly, I haven't turned my synch saves off myself... but I do remember reading a doom-sayer saying that if you did, and then turned it back on, you stand a good chance of losing save files. Maybe even the important ones that you want to continue.
Wish I had a more definite answer for you. Well, since the new patch is coming out soon, maybe you could take one for the team and find out
I think a lot of people will be wanting to start a new campaign once the new patch is out anyway so now might be a good time?