First, it seems you are confusing the OFEV with the Generic Patcher, a big error, because you should not touch the Generic Patcher except doing what's in the install instructions.
OFEV: In some tabs in the OFEV you can change TWoS to your taste, but you will do fine if you don't change what you don't know. Consult the Sticky Posts for more details, start slowly, SH5 ain't easy...
Once you have made changes, you can only save 1 TIME when the program is open, or you must restart it.
And no, the OFEV will not mess up your savegames, there are plenty of other causes for that
(let me guess: you didn't save/reload after going in the bunker when starting?), and to be sure nothing in the OFEV is screwed-up there is a *.bat file with which you can reset all settings to Standard, better use it if you have done changes blindly! And if you did mess with the Generic Patcher, then better do a fresh install after deinstalling SH5 and wiping all file/folders, inclusive savegame folders.
.
XS