After reading a few more threads and doing research, I think I know what I need to do now- if I manually remove the ids then new mods will replace those blocks. I guess what I can do is force delete the ids, copy + paste my base into a new world using the same seed with the current mods, then I'll have free ids and shouldn't have issues provided none of the blocks from my old mods are near my base.
In theory I'll be able to update/add mods again... I'll try in a little while and post what my progress is.
Do I need to delete the 'BlockedItemIDs' file in level.dat to free up the block/item ids? I can't find anywhere else they could be located...