I also use woods like this, and the first question is ‘can I change the position so that it is not an issue?’. So is it possible to flip the piece and have the resin pocket away from the top or outside of the workbench.
If it has to be on a work / show surface, then I would try to use a skewer or nail to remove as much as I could. If you get enough out, then sand/saw dust can fill in the void. If you have the time, stand the piece vertically, somewhere warm, put some tape at the bottom edge of the pocket, and some of the resin will flow out naturally.
Colin, Czech Rep.