Right on. You know for next time
I like simple. Just let it re-copy rather than mess around with ID's.
1) You KNOW it's going to work
2) everything is fresh, any issues (not that there were any) would be gone.
3) You can take the time to fix your naming conventions on your copy jobs if you want.
4) You can modify the copy jobs, (add multiple jobs to one copy job etc.)
5) Use the throttle if you are saturating the pipe, if it takes 4 days, who cares. (unless your business is strict about that).
For the last point, it is what it is. It's not your fault and it was caused by the VMware software install. You won't get in trouble for that. To go one step further, if the incremental are going at your main site, they should get copied as well so you won't "lose" any days. the ONLY thing would be if a DR occurred like right now. but I'd say the odds are in your favor, and not much you can do about that.