It doesn't stop the fact it was already order that all the FEV was order to sent to Mariposa Base beforehand in http://fallout.wikia.com/wiki/FEV_experiment_disk#Log_Date_January_7.2C_2077 and if by theory that Vault Tec do have a sample of the FEV, then the Enclave would have known about it/have the sample and have put its experiment to use earlier than it was in Fallout 2.
As if secret shadow government projects don't involve lying and deception. Just from Fallout 1&2 that document is false, not all the FEV was moved to Mariposa. Remember the lieutenant from Fallout 1? And his theory as to why vault dwellers made the best super mutants.
When the bombs hit the original West Tek Research Facility creating the Glow, it released FEV into the atmosphere, the radiation destroyed the mutagenic effects but it did partially inoculate any person against additional exposure. This inoculation was passed onto their descendents as anti-bodies often are. As a result most wastelanders produced stupid mutants and the master sought out the vaults as they contained people without radiation exposure and with out previous FEV exposure it worked for both theories.
The exposure from West-Tec being bombed is proven true in Fallout 2 when the Enclave makes their targeted virus to wipe out the main land. They designed it to effect wastelanders but not a pure strain of humanity. Hence why they tested it on the residents of vault 13 and Arroyo.
If your note was correct than the Enclaves virus never would have worked because it couldn't tell the difference between a wastelander and a "pure human"
if by theory that Vault Tec do have a sample of the FEV, then the Enclave would have known about it/have the sample and have put its experiment to use earlier than it was in Fallout 2.
How so? Vault 87 was struck directly by a nuclear weapon at the onset of the war. The Enclave's ability to monitor that vault may have been damage thus they didn't know about the progress of the FEV experiment in that area.
The idea that the Enclave DIDN'T know about the FEV experiments is ridiculous. There the secret evil shadow government of course they knew but that doesn't mean they had a sample on hand.
Here is the absolute fact, had Black Isle continued making fallout games they'd have invented a brand new source of FEV to continue using super mutants as enemies at some point. Hell the master was supposed to have spent years experimenting with FEV in order to make the super mutants as we know them in Fallout 1. Yet the Enclave does it by accidental exposure in Fallout 2? why do they get to rewrite the rules from fallout 1 to 2. but not when a new team takes the reigns. So the new source of FEV was inevitable it was going to happen eventually/