@Ink, thanks for asking. Short answer: yes.
During a longer travel with my Le Requin (planned from Little River to Galdonas, for grinding easy XP with my PvE account) I reached the much desired Commodore rank (Santisima!) and stopped my travel at Mayaguana. There I checked out the new UI (very nice), found the 2000 Doubloons in the redeemables list (even nicer) and claimed them.
Then I left the port (I have no outpost in Mayaguana, it just was easy to reach and neutral) and went to Saint Ann where I rebuilt some mines. From there I wanted to teleport ("transport") to Kingston, but I couldn't pay the cost because I had 0 Doubloons. WTF, I should have had 2000? I asked on Steam forums and here, I got the hint I should check out my chest first - it's empty - and the warehouse where I claimed the Doubloons, but knowing that all stuff always would have vanished when leaving a port without having an outpost there I expected to find nothing in Mayaguana, and so it was. But when I left Mayaguana before right after claiming the Doubloons I can't remember reading a warning like in the old and simple UI - there always came a red warning not to leave stuff in the local warehouse without having an outpost! I had no clue that I had to put the claimed Doubloons from the warehouse to my chest manually.
That's probably how I lost my 2000 Doubloons. 😕