Hi Chris,
even though this post is quite old, it may still be relevant. Just a quick understanding of what you're doing because I've had something similar-ish:
You have a SQL/Exchange server. Do each of these servers have a single vmdk with multiple partitions, or do they have seperate vmdks for each partition/drive that's configured?
The reason I ask is because I believe I had something similar happen...
I have a SQL server configured with 3 seperate vmdks representing each disk drive in the O/S. I ran the mbralign tool against all the vmdks seperately with no incident, but when I rebooted the VM I found that SQL wouldn't start. After some investigation I noticed that except for the boot partition, the LOG and Database drives were not even showing in the VM - hence SQL may still be installed, but the databases and log files don't exist any more.
What I believe is happening is that when you run the mbralign tool against the boot partition/vmdk, it aligns it, and somehow updates the identifier for the vmdk. No problem when you have a single vmdk, or when the vmdk you're aligning is the boot partition, however, when you align your secondary and tertiary drives, they are also somehow modified so that the vSphere configuration no longer shows those drives and doesn't load them ie:
Pre-alignment:
drive1 = id1
drive2 = id2
drive3 = id3
Post-alignment:
drive1 = id4
drive2 = id5
drive3 = id6
but the configuration of the VM itself, expects this:
drive1 = id4
drive2 = id2
drive3 = id3
My experience with this was quite strained as my SQL server also contained the virtual center database which in itself had it's difficulties. I still haven't re-aligned this particular SQL server but when I do, I believe that aligning just the first drive will do the trick.
Regards
Asaf