[I picked up this thread today because of some issues I experience with my MESU, SiTech, PhD2 combination. (My calibration is all screwed up, and my Mesu's RA tracking appears not to be working correctly. -- Off-topic here.)]
Did you ever solve the problems with your EAGLE?
For what it is worth, I had weird problems with USB, EAGLE 2 Pro and SiTech/Mesu. I solved them by updating all SiTech software, drivers and firmware (3 pieces of SW if I recall) and, most importantly, by updating EAGLE Manager to the latest version (2.7). I had been running 2.3. PrimaLuce confirmed that the Eagle software used to have a technical issue managing USB ports reliably. For my set-up these sporadic "SiTech not reconnecting to COM Port (EAGLE USB)" went away completely.
See here for Eagle Manager download page: https://www.primalucelab.com/astronomy/downloads
Apologies if this issue has been answered or has become irrelevant at this point.
Kris