The generator is 480 volt to a transfer switch, then to a disco, which feeds a step down transformer (step down to 3 phase 208/120 volt) with the neutral coming off the x-o lug of the transformer. The customer wants to refeed an existing panel off the generator panel and abandon the existing feed(when all is ok with the poco feed the generator is on standby, and when they lose power the generator kicks on). my question is this, If I leave the emt connected to the existing panel, will I be creating a hazard(since there will be two ground paths going back to the main switchgear?
I presume that you are asking about leaving the EMT connected, but that the feeder (and thus any ground/neutral bond upstream of the feeder) will be disconnected.
I don't believe that this will result in any significant hazard, and don't believe that there is any code violation. What you will be leaving is a loop structure in the non-current carrying bonded metal. While this is a violation in current carrying conductors (unintentional parallel paths, parallel paths through equipment grounding conductors, neutral to ground fault, etc.), it is expected in non-current carrying metal.
The only time in code where loop paths are to be avoided in conduit systems are when current carrying conductors are not carried in the same conduit as their 'anti-parallel' conductors (I'm trying to come up with a general term for the complete set of conductors comprising a circuit which carry net balanced current. Loop paths that include unbalanced current carrying conductors become transformer secondaries, and can carry considerable current.
Only in some rather specific examples (MRI rooms, certain communications facilities, etc.) is a particular attempt made to insure proper star grounding with no loops, and this is not a considered a safety issue, but a design issue.
I suppose that in an environment with particularly strong and changing magnetic fields, closed paths in the conduit system could become a safety hazard; this is the issue with unbalanced current carrying conductors, but it might be an issue with high field magnets for research.