This nearly happened to me, and still might knowing my luck. I saw my challenges didn't load, so I backed out, shat myself, kicked my brother off the internet, plugged an ethernet cable from the Modem into my 360, reconnected and they didn't load...
Until I checked my Syndicate, then I went back to my Agent tab and they had reappeared. I only really have Electric Armour Kills to grind out, but I'm terrified of booting it up again in case it wipes everything. Such a great game, but the glitches, especially this one, are soul-destroying if you get hit with them.