I don't have an aux tank, but I'm been on this forum for over 14 years . . .
Discussions on this topic, even years ago, suggested that GM put "sanity" checks in the some of computer programming. So, if you're driving along and the fuel tank is getting fuller . . . insanity!! . . . so it knows something is wrong. To be safe, it would set the fuel gauge to E since it lost confidence in the sensor reporting.
The easy solution is to only transfer fuel when parked (rest area, lunch, etc., when traveling). Or if done while moving, accept that it might complain and set codes and point to E; then just reset (if codes) at some convenient time later, and I would expect the fuel gauge would come back to life, too.
2004.5 Silverado 3500 SRW 4x4, D/A (LLY), Ext. Cab, Long Bed
TxC V2 aux radiator w/Fan (leaked after 12 yrs
), engineer837 aux rad
, TxC CAI, LBZ MP, Scangauge II, Nicktane aux filter head, KD lift pump, 2008 PS pump, 2011 hydroboost, Frederico Swaybars, Rancho 9000XL, Torklift StableLoads, BFG AT/KO2, Lance 835 Camper often in the bed.