Yes. There were four varieties of rebuilt GP30 on BNSF - Santa Fe in-house rebuilds, plus BN had GP30 and GP35 cores done by three builders and each had a different last letter in their model designation. AT&SF units became GP30u and GP35u; BN had units rebuilt by EMD, VMV (Paducah) and Morrisen-Knudsen, so you had GP39E, GP39V, and GP39M. Eventually all were reclassed GP39R. The most amusing include EMD rebuilds of a batch of former Southern units - they retained the GP30 long hood, but got an entire new GP35-style cab and short hood with low nose.
Internally all seemed to get more or less the same modifications - electrical cabinet upgrades and 645 power assemblies in the 567 block, remaining at a 2250 HP rating.
Units in Santa Fe paint were always Santa Fe units, but any showing up in BN/BNSF colors could come from a wide variety of predecessor roads including some former CSX (SAL, L&N primarily), UP and IC/GM&O units.