The Gerber format does indeed allow pads to be defined with an internal hole. However, since in isolation milling you normally use Gerber files to mill the isolation contour and Excellon files to actually drill the holes, isolation software normally ignores those pad holes in Gerber files exactly because you don't normally mill them as contours (I just tested this with FlatCAM - holes inside my Gerber pads were not displayed, I had to load up the Excellon file too for the holes to show up). I have no idea why FlatCAM would want to mill them out if that's indeed what's happening - it would help if you could post your file (or even just a small portion of it, if you'd rather not put the whole file on the internet). Anyway, stressing again that this is not supposed to be necessary, there is a simple way to "delete" holes directly from your Gerber files: you just have to use a text editor to open them (Gerbers are actually text files), then look for a bunch of lines like this at the top:
Code:
%ADD10C,0.006000X0.003000*%
%ADD11O,0.086600X0.059100X0.030000*%
%ADD12C,0.059100*%
Basically, you're looking for lines beginning with "ADD". The hole itself in the pad is described by the last number in those rows that actually have a hole included - you can just delete the number and the preceding "X". Lines wit "C" codes (circles) must have at least on number (diameter), those with "O" codes (ovals / obrounds) must have two (width and height) and so do "R" ones (rectangle). Anything more is the diameter of the hole, like with my first and second line. De-holed they would look like this:
Code:
%ADD10C,0.006000*%
%ADD11O,0.086600X0.059100*%
%ADD12C,0.059100*%
Still - you're not supposed to have to do this. But if nothing else helps, you can easily try it. Good luck!