A little nervous about upgrading to 8.1

I'm currently downloading the update now but confess to being a bit nervy as to whether I should install or not.
I have a MacBook Pro retina and I have Windows 8 installed EFI booting (not BootCamp).
I'm wondering about a couple of things.
Will the upgrade realise it's an EFI install?
Windows 8 on a Mac with EFI booting is notoriously finicky about writing and changing the BCD. I suspect a problem there.
I also have a program installed that I cannot install again as the supplier is now closed and further activations cannot happen. I have fears for this program too.

Decisions, decisions :huh:

Oh, I've been moved.

Well that was an experience!
Downloaded ok, installed ok then rebooted about 7 times in total.
Tried to setup hardware 3 times.
Tried to recover system twice.
Rebooted 3 more times then told me it was trying to recover my previous sytem!
It eventually told me that it couldn't update me to 8.1 due to error
0xC1900101-0x40017

whatever that may mean

At least it seems to have recovered Windows 8 Pro intact!