They are definetly strange creatures. I don't have a BTA, just a Condylactis which I think is a bit hardier, but not sure on that. Mine will be looking like the loch ness monster for a few days, then will have one of his shrunk up, look like hell, bad hair days. Used to scare me, but now I just ignore it mostly. I do check my water out if he goes like that for more than a day or two. Kinda like the canary in the coal mine, but usually the water is fine. No idea why it does this, but seems to be normal behavior, at least normal for my condy.
Zenn, how is his attachment to the rock? If he seems to have firm attachment then it might not be something to be too worried about. How long has this been going on? I know mine is not concerned about food at all when he's in his "shrunken" phase. I was thinking that maybe periodically they do a purge on all the old water they have inside or something along those lines. No way sure about that one, but was just thinking that could be a reason why mine periodically looks like he's gonna die. Hope that it's just a similar thing with yours.