Quote: "I have a question about mods however, as I find they have many interesting features that may be of good use for my game. If i were to save my game in a modded version of FPSCx9 would I still be able to open it in the unmodded version afterwards? Or will there be compatibility issues?"
You might get lucky and be able to save in modded and open in unmodded, but any features (scripts, etc) that are in modded will not work in unmodded. Also recognized that save/load routines usually get altered around between modded and unmodded, which leads to massive issues when trying to load a modded save into an unmodded variation. For example, variables that may be used in modded version that do not exist in the unmodded; you attempt to open that save with variable usage in unmodded and it does not load; doors not opening properly or appear open but you can't pass through them. I could list more examples but you get the point.
There's no problem that can't be solved without applying a little scripting.