We have a new commercial loan that is secured by a mobile home that has had its tongue & axel removed. Does that make a difference in how it is classified - site built vs manufactured home?

No, removal of the axle only makes the mobile home a "permanent" fixture on the site. It does not impact how the "building" was constructed, which is what site built or manufactured refers to.

What is the purpose of the loan? Also, just because the wheels and axels have been removed, it does not mean it is no longer personal property which would mean that it is not part of the real estate, unless the title has been retired under whatever process that is required by your State law.

You need to know the legal status of the dwelling. It is either personal property (still titled) or part of real estate. That can determine what sort of documentation you deed (personal property collateral or a real estate mortgage) and what form your disclosures will take (TRID or not TRID).