Lee are a well established, reputable company - I don`t think they`d supply their excellent filters in a package that would cause damage to them.
I used the pouches you mention for quite a while without any problem before getting a zip-up type wallet with multiple pockets - a bit like one of those CD wallets (also made by lee if I remember correctly).
Truth is, if your filters get dirty, continually sliding them in and out of ANY type of pouch/wallet (no matter what it`s made of) is potentially going to scratch them.
Believe me, they`re going to need replacing sooner or later no matter what you do (depending on the amount of use they get and under what condition you use them, obviously). Consider it as another of those photographic `expenses`.