I added some code to my copy for this, and once I'm finished testing I plan on attaching a diff here for it (unless it just isn't getting added). Basically I added a variable to track how many karma have been discarded, the variable is incremented when you discard a karma (this is done in GenericRequest.java, maybe it should go somewhere else, but karma is in the ItemPool and the variable is in defaults.txt). Before you jump through the gash, if you have any karma and you've discarded less than 3 you get a reminder message. When you ascend, the variable is reduced by 3 or set to 0 as appropriate, but I can't test that part until I ascend in 6+ days (grrr carboloading).
I wanted the reminder list to have a link to discard a karma (with the confirmation popup of course), but I couldn't figure out how to add the password hash to the link, so for now it just links back to the right inventory section.