FQDN == Fully Qualified Domain Name.
A Fully Qualified Domain Name is the host's hostname with the domain name appended.
Sounds to me like you don't quite understand how DNS works, which is making it hard to figure out what's really going on here, honestly.
As pointed out by @jimbobmcgee 's answer, it is possible to keep the DNS suffix the same when joining the computer to your AD domain, but DNS suffixes and FQDNs are different things, and I think you're confusing the two, which is causing issues in addressing your question.
There's no reason that you can't have the FQDN change and still do what you're doing. (I think, based on your description, anyway.) The easiest solution would be to setup aliasing in AD DNS so that
vm100.eng.mycompany.com point to the same IP. In all honesty, it seems to me like your system's a little broken/misconfigured if it's running against a different domain/subdomain than the one you're actually using, and I'd work on fixing that, but there are any number of quick fixes to alleviate the symptom you're encountering.