Hmm, this doesn't sound right to me.

Pectin in your wine, in my experience, stops the wine from clearing.
If the wine has cleared and then become cloudy again I may be wrong,
but I doubt it would be pectin. Also I beleive that pectin clogs
filters so if the wine ran through the filter...
I think it must be some form of instability; acid, tannin or protein
maybe, but I have no experience in fault finding these and without
knowing your process and all the ingredients in the wine, it would be
difficult to work it out.
Apples contain malic acid which could be attacked by bacteria causing
a cloud, citric acid can also suffer bacterial breakdown. Tannin can
also produce hazes but I dont think Granny Smith contains that much
tannin.

If it were my wine I would put it all back into a bulk container and
keep an eye on it, it may just need more time to re-stabilises and may
well drop clear in a few weeks.

Meanwhile post more info on your methods and see if anyone else comes
back to you.
Denis