Xenon does not rebuild 7th Wharf.

[PV_]

6.20 - no mods - all DLCs (perhaps important for this particular case).

Xenon never rebuilds 7th Wharf. Limit is 6. But does rebuild all 7 shipyards.
Oversight with number set for XEN Wharf limit, I suppose.

In the save file below everything prepared to teleport PHQ either at XEN Shipyard or Wharf at Matrix 598. Tests shown that Shipyard always gets a plot in the time below 14:00. Wharf - never, no matter how long I'm waiting (SETA used) and how many attempts undertake.
Brand new 6.2 budgeted start. The very beginning since world generation. Also I run SETA at Pegasus to keep related sectors in OOS state.
Save file.

Let me know if you need a save after some time beyond Wharf nuked (specify one, pls) you may consider as enough to make a conclusion.

#Remark
ZYA War forge never in construction if upgrade is made from version below 6.0. Its okay. Nobody guaranteed 100% transition compatibility. Just saying in case you may afford to investigate the issue. I assume problem is in a script which activated "on station destroyed" and since Forge never destroyed (as it never existed in the first place) script doesn't launch.