Cia's are region locked sometimes. They might also work as 3ds and not for cia for any number of reasons.
Anyway, back to the op. I've manually done a cia--> 3ds conversion by finding the ncch's inside the cia and extracting them with a hex editor. Then I rebuild the ncch's as a cci with makerom (3ds).
This process would certainly be easier if there was a tool to dump the ncch's from the cia, but there doesn't seem to be any. I've looked all over. (and no, makerom's cia->cci is broken)
Well to play .3DS format, I'm going to assume that OP has a flashcard. And since well gateway is the most popular i will use that example for this post.
With a .3DS rom it needs to be played from emuNAND or 'gateway mode' if you don't bother with emunand. To boot emunand or gateway mode you must have the red card inserted right? So you may as well just put it on your flash card and press select and navigate to the rom if the red cards already inserted, right?
Creating .CIAs are much more involved than the steps i posted above.
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Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)