Bet you a nickel he was killed off-screen by the Ori when they took the planet.
Well according to producer Joseph Mallozzi in a blog entry from some time ago, he said something like 'I always imagine Jonas is fighting the good fight in a fun resistance-based story'. Dig it up if you'd like, but I sort of took that as close enough to canon since it came from one of the main guys on the production staff.
Didn't RDA have a big problem with him? I'm almost at Season Six, it'll be interesting to see how that affects the episodes.
You know, I've read accounts refuting that on multiple occasions. I don't think anyone has ever had the courage to straight-up ask
RDA about it, but Corin has denied there was any sort of fiasco and Amanda Tapping has as well. Corin has always sounded nothing but positively gracious for his time on
SG-1 -- a real stand-up guy considering he got stood-up in season seven.
It ultimately boiled down to this -- Daniel Jackson (and Michael Shanks by comparison) was a much more recognized and universally-accepted character and when Shanks wanted back in with the seventh season the writers were committed to making it work no matter what. Since Jonas was getting a mixed reception from the fans and at least in concept he was undeniably a replacement for Jackson, he got reduced to recurring status and then disappeared by season eight.
Back before season ten TPTB were very insistent that a five-person team would just not work dramatically, so it kind of irks me (and a lot of others) that they eventually tried for it but Jonas got the boot such as he did.
I'm just thankful this all happened a couple of years before
SGA's Ford debacle. By that point in the franchise TPTB had gotten so full of themselves and their 'we can do anything we want to these characters in the most ridiculous ways and still get rich off of this' mentality that
SGA really suffered a bit of a revolving-door problem.
The writers felt like Ford wasn't working out after season one (a point contested by a
lot of fans on GateWorld, but to be fair, that happens with everything) so they gave him an arc that played out fairly interestingly but then dropped his character without a feeling of proper resolution.
And then Weir... ugh, don't get me started. Jonas Quinn was treated like a god compared to what they did with franchise characters later on.