Use ALLISON filters and it won't be an issue. I know that the ones you get from AUTOZONE were said to have problems with the magnet blocking the flow through them. Use genuine ALLISON filters and it isn't an issue, and they aren't that expensive from an ALLISON dealer.
1995 GMC 2500 SUBURBAN powered by 01 DURAMAX/ALLISON, 3.42 gears, 261 T-case
Trans has a mild build with ALOT of help from MIKE L. which included ALTO's for C1-C4 and a PI ML converter
DIAMONDEYE 4" exhaust with a CORSA muffler, AFE stage 1 dry filter, EFILIVE, KENNEDY single pump and pump rub kit.