Just realized I've been addressing the wrong problem. (My apologizies, BushPilot. You were on the right track.)
eBattle, you used SEQU->SEQM as an example along with PV4. SEQM is a PV5 airport. Presumably, you wish to use SEQM as the ICAO but AIFP, with PV4 as the designated Target Version doesn't "know" about SEQM, is replacing all instances with SEQU. (SEQM was not introduced into Flightsim until PV5, shortly after the real SEQU was closed and replaced by the real SEQM. But, since PV5 doesn't appear on the AIFP dialog, you are unable to select it as the Target Version. An easy workaround might have been possible six months ago.)
So how is AIFP to know about SEQM (position/elevation) if you are using PV4? The only way is if you Collect Add-ons (including SEQM for PV4) - which may be what you mean by "I've tried updating/adding my scenery within AIFP" and enabling one of the options in the Airports menu applicable to add-ons.. But, since you didn't say so, I don't know that.
By Collecting Add-ons and using the various options in the middle of the Airports menu, you should be able to do exactly what you want to. If SEQU/SEQM is the only airport of concern, simply Kill SEQM. (Do you really want both airports displayed by Flightsim?) Otherwise, designate alternative ICAOs.
Notwithstanding the foregoing, assuming you have one of the two options for add-ons enabled, if Alternate ICAOs are not being processed by the compiler into the traffic file, please send me files I asked for in the earlier post and I'll investigate.