I'm not sure I understand exactly, but there are a couple of things to think about. (This assumes that Texas UCC 9 isn't differernt from the standard). Also, I am not an expert or an attorney.
A Purchase Money Security Interest (PMSI) will take priority lien over a general "Equipment" filing. However, the burden of proof is on the PMSI institution to prove that the funds disbursed went for the purchase of the specific equipment. Generally, this would entail a payment directly to the dealer or something similar.
Now it sounds like in your case, you're going to get an assignment of that UCC filing from the other bank in a refinance? I don't know if that would work to retain a PMSI position or not. I don't think so. Generally, with a PMSI loan, as the principal is paid down, your lien amount decreases as well. So even if you have a PMSI for a $100,000 tractor, if they've paid it down to $10,000... that's the maximum value of your lien.