Wasn't this is the time period when Holly was being hunted for murder she committed as "Catwoman" (bogus and eventually proven so). If so, Holly could have been on the run at the time. Karon didn't seem the type to bail because of the super-hero life. She's seen Holly (and Selina) at the worst. I hope they haven't officially broken up.
Or it could be I'm just mad that Rucka seems to have broken the long-term relationship of Maggie Sawyer and Toby just to make Maggie a love interest for Kate Kane. I would hate that. Because apparently Maggie and Renee are the only two other lesbians in Gotham, if you read the Batbooks (not counting count Holly/Karon).