I have tried that type of storage as well, in addition to the non-waterproof issue, the material on each fly get compressed and contorted after a while when you have quite a few stacked on top of each other.
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I am still not a cop.

EZ Thread Yarn Balls

"I don't care how you catch them, as long as you treat them well and with respect." Lani Waller in "A Steelheader's Way."