Ouch! That sucks.
That's exactly the reason why I suggest using 2 pin spanner wrenches -- one on the end cap and one on the diaphragm clamp...just in case they get stuck together. In my experience, it's pretty common to see those parts fuse together due to corrosion, particularly if the reg hasn't been serviced in a while. That connection is a metal-on-metal contact point.
FYI, the Zeagle reg tech manual indicates that the Flathead VI-specific pin spanner wrench (P/N #347-0003) be used on the end cap and the "general" pin spanner wrench (P/N #347-0001) be used on the diaphragm clamp. I could be misinterpreting the manual, but the instructions suggest that technically you need both sizes of pin spanner wrenches to work on the Flathead VI first stage.
Good luck with everything...