If I understand this correctly your using TortoiseSVN to update right? If you made NPC's and quests you like to save just right click on the appropriate quest/npc in the directories such as /eqemu/quest/zonenamehere/questcharname and chose the TortoisSVN and ADD TO IGNORE LIST. When you update the files next time it will ignore any updates on this item.
If it is items such as new sword etc you need to save the SQL info and such.
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