Yes, if the anchor icon is removed from your home base then the Japanese most probably captured it or an order to relocate base of operations was sent out. You don't always get the message. I'd look for the closest allied base and dock there. That happened to me at Cavite Base in Manila, there were friendly ships there but no docking options. I had to make it to Java instead. When I ended the patrol and back in the office the log book stated base of operations was changed.
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