It still didn't work as needed. That didn't remove the bases after the +N. However it did help me a lot and I managed to get a version which does indeed work as I want it (prints just to keep me in clear that what happens is indeed what should happen). I also added the || last to prevent that eternal loop you mentioned.

  while (m/[+-]([0-9]+)/g) {
    printf "pos ($1): %d -> ",pos($_)-1;
    pos($_) -= length($1)+1;
    printf "pos ($1): %d\n",pos($_)-1;
    s/\G[+-]$1[ACGTNacgtn]{$1}// || last;
  }
[download]

So thanks for helping me out on this :).

Though on the whole. I think that the (??{...}) would be best choice as repositioning the pos() is probably not a good idea in general. Note that I included the negative as well as positive match in this as that would remove the next regex I have :).