Simple, if you have only file changes that don't require compile (multisells, texts, quests, events, mobs, configs etc.) copy them in a different file.
If you have made changes to the code, the safest way is to create a diff file in Eclipse (I have seen a topic about it in here somewhere, search here or in google), check out entire version, apply the patch and only check things that aren't exactly as they should be.
After all of the above, compile, extract, paste old files in their correct place, run the database installation, select to update the database, not full install and, provided your custom files are not extremely out of date, you are done!
Ofc you could just have used search in the forum and get the above answer, possibly even better explained...
