Same goes for the cheat/debug package script, the "add ship blueprint to HQ" command will only affect the last HQ you have placed.
There can also be some slight issues with commonly used community scripts such as Lucike's (confirmed for prospector, not sure about CAGs), and possibly some other station trader scripts: long story short, automated traders set to being homebased at (and thus managing) a PHQ might get confused if there's more than one around (especially if they are in the same sector).
With Lucike's prospector, for instance, if you have two HQs in the same sector and give each a dedicated miner, these will both try to unload at only one HQ: the miner homebased at that HQ will work fine, but the other one will get stuck unable to unload (as if the station cargo was full) and send you a message.
Definitely nothing gamebreaking, but it might give you some headaches along the way, just so you know
