After experiencing random freezing, I read that I might be able to fix the issue by using Windows 98 Combatability mode. However, once I did this the game no longer detects my save file. Can anyone help me out?

That's weird. SR2 puts save files in My Documents so they should be available regardless of the mode. You can try avoiding the Win 98 compatibility mode and just set the affinity (see stickied thread for details).

how do i set the affinity?

Simple affinity check doesn't work as intended on all systems, so you can use a program called StartAffinity, or if you are on Win 7 you can make a batch file.

i solved this problem by playing the game on windows 95 mode
and then played to the first savepoint
then seeking the direction of the new savegames and then copying the old ones into the new direction and it works
it seems that when using windows 98 or 95 mode the system uses another savegame directions
so u don´t neccasserily need to set affinity ;)