well unfortunately they rain flies are originally silicon impregnated. this not something you can do yourself . . .
the only other advise i can give is to ask this same question on a backpacking forum; there tents are far more expensive and they may know another way.
Interesting.
I didn't think that this would be important, but maybe it is. I'm looking at my Hannibal roof tent that has a nylon fly of some type, and a large privacy room made of the same material I believe; replacing these is not in the cards. I have just a few sections of both that are not repelling the water very well, and I'll be damned if I didn't have to camp in the rain two out of the last three trips so I'd like to do a little maintenance. I'll pose the question to Hannibal, but I'd figure someone must have some more insight.
I assumed re-treating your nylon fly and other things like a jacket/shell would be common.
AutoHome does post this about their tents:
http://www.autohomeus.com/info/care.php said:
To restore [water repellancy], use 303 Products' High Tech Fabric Guard according to directions. Let dry thoroughly, then rinse the tent again and let dry in open air.
High Tech Fabric Guard is not a silicone based product, but solvent based.
Before going further, I think I'm better off inquiring to Hannibal.