Dear Styg!
On my last playthrough i found a glitch. 
I started expansion, found Phil's arm, then moved on straight to Lemurian Health Centre.
In healthcentre i tried out two thing:
 - first one was to remove chip from Phil's arm, then implant it into my hand, and go back to Aegis camp to open Arch Keep - i couldn't open the door by any means. Dialog was stuck on bringing a working chip, quest was marked as unfinished. 
 - second try was to extract RFID from Phil's arm (without implanting it into my hand) and bring it back to Aegis camp to open Arch Keep - after talking to Professor, quest got marked as completed, but dialog was stuck on bringing a working chip. 
If Phil's hand wouldn't be lost during extraction of RFID chip, both problems could be solved at once.
Cheers,
Hipsternity