Shouldn't be any problem having both installed at the same time. May be some weirdness with playback or recording if both are running at the same time, depending on the driver and audio device, but nothing that can't be handled.
If they can share what bugs they believe will cause problems, I can look into it further.
By 'engineers' I'm assuming they are train drivers and hence can be forgiven for not knowing that all versions of Audition (and even CEP) can all live happily on the same machine.
Audition 3 was the last version to open an ses file. Later versions of Audition will open a Audition v3 xml but without fx
The tool you need to do the conversion is http://www.aatranslator.com.au/ses2sesx.html (I think it's still available)
If you find it useful consider making a donation
If you need to convert from sesx to ses then you will need www.aatranslator.com.au but it doesn't convert fx
however our engineers believe there are bugs with having both versions installed.
I should get some new 'engineers' - preferably ones who know things as a result of sensible investigations, rather than guessing believing them to be the case.
The simple fact of the matter is that all versions of Audition that are supported by any given OS can exist on a machine, quite happily, at the same time.