The tube pre-amps which invert phase basically swap the positive and negative terminals on their output from their input. I am not sure if the 990 will have an issue with that but it is possible that it will not pass the signal backwards. I would think that it would have no issue since it is sort of like swapping the red and white leads on an analog input. The 990 probably won't have an issue because I have swapped the left and right channel leads before to try to isolate an issue and both channels put out the same sound but reversed. I assume by the term "using the 990 running through the new preamp" that the tube pre-amp is feeding the 990 through an analog input and then to the main amp. I am not familiar with the pre-amps above but I would expect that either the volume control on the tube preamp or the 990 would have to be set in a position for the proper gain. If the tube pre-amp has an output path that can connect directly to the main amp that might be a solution since it has a volume control on the preamp.
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Music system
Model 990/7500/Magnepan 1.6 QRs/Technics SL1200 MK2/Aperion S-12 Subwoofer/OWA3/Sony NS75H DVD
APC H15 Power Conditioner
TV System
Large Advent Loudspeakers/ Polk center/Monoprice surrounds/Panasonic Viera 42 inch/Onkyo HT-RC260/Sony BDP S590/Directv
Home Theater System
Onkyo PR-SC886/Outlaw 7125 Klipsch RF-82 L/R,RC-62 center, RB-35 SR/SL, BENQ HT1075, Outlaw LFM1-EX/OPPO BDP-83/Directv
Harmony ONE
Blue Jeans and Monoprice interconnects
APC H15 Power Conditioner