I'm looking to power a 3 phase compressor 80 Amp from 2 panels individually fed from different transformers and only have a 3 pole change over switch. If I link the 2 Neutrals will I have problems with back feeding?

A 3 phase unit should not need a neutral, so there is no need to "link" the two neutrals, which should not be done anyway. Each neutral from a transformer is dedicated for the load of that transformer.

If for some reason your 3 phase AC unit does need a neutral, then a 4 pole "change over switch" (AKA Transfer Switch) will be needed so that each respective branch circuit ungrounded phase conductors utilize the respective neutral.

[QUOTE=tkrussell;1605944]A 3 phase unit should not need a neutral, so there is no need to "link" the two neutrals, which should not be done anyway. Each neutral from a transformer is dedicated for the load of that transformer.

If for some reason your 3 phase AC unit does need a neutral, then a 4 pole "change over switch" (AKA Transfer Switch) will be needed so that each respective branch circuit ungrounded phase conductors utilize the respective neutral.[I need single phase for controls and condenser fans on the unit and am aware that a balanced load needs no neutral. I was of the opiinion that I could link the neutrals because both transformers are being fed from the 1 original incomer. 10kv at the incomer split to feed 2 transformers to step it down to 400v where the single phase operating voltage is 230v]

Each transformer is a "Separately Derived System" at the secondary, and the neutrals of these transformers should not be connected.

A better solution will be to have a small control transformer in each AC unit for control voltages.