Creatures Caves

Does anyone else have a hard time getting C3/DS to recognize when an agent has been updated? Sometimes, if only the code has changed, I can get it to see the update by using PRAY REFR, or by exiting the game and restarting, that sort of thing. But not always -- and if the .c16 has changed, I have a HECK of a time getting the new agent to work, because the program simply insists that it's not there, or tries to keep using the old one, even if I've deleted it from the directory.. Are there any tips/tricks out there, or am I the only one with this problem?

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Optimist: the glass is half full.
Pessimist: the glass is half empty.
Engineer: the glass is twice as big as it needs to be.