My DA:O Fixpack is very humble. If my Fixpack modifies a file, and any other installed mod touches the same file, that other mod’s file will get priority and override mine by default. If this happens, the fixes my mod makes to that file will not work, but it maximizes the chances that the other mod will work without problems. That’s no guarantee, however, as another file somewhere else in my Fixpack that was not overwritten may be dependent upon the changes in the file that was overridden. So, add files from other mods that are also in my Affected Files List with great caution. Note that if you overwrite player_core.nss, as a number of combat mechanic mods do, you will only lose my Soundset fixes (GL3002) but it should otherwise work without additional issues.
I always encourage starting a new game after applying my Fixpack, as installing it mid-game always has the potential to create unforeseeable issues that may not be immediately obvious. During development of v3.0, I rewrote every fix from older versions, and internally versions 1.0 to 2.0 are considered a completely different mod from versions 3.0+. Nothing from those older versions will transfer to version 3.0.
If you *must* try to apply my Fixpack (or any other mod that affects quests) to an old save game, you can minimize the possible negative consequences by first finishing off any side quests you had open in your journal that are affected by the mod, and any main quest areas (especially Orzammar) that you’ve visited previously. Basically, load your save game, finish up as many main and side quests as you can that take place in areas you’ve already visited, THEN apply the Fixpack. Again – none of this is recommended, you’re always better off starting a new game as there are many fixes in the early game that have ramifications later on, but if you must, this method gives you the best chance of avoiding problems with quests. Even that will probably not be enough to avoid issues with fixes applying to any followers that have already been recruited, however.