The Navy probably already knows about the base. They don't really go into details in BOTP, but in Gatchaman the ISO (International Science Organziation) runs the base and team operations.
In BOTP, the base was eventually found by Spectra, but it is not the "primary" base that gets hit. In the epsiodes "Attack on Space Center pts 1&2", Spectra destroys the secondary base of G-Force, not Center Neptune.
In the original Gatchaman series, Crescent Coral is the only base that the team has and Gallactor destroys it. The team doesn't get a new base until the start of the second series.
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