Any suggestions appreciated Jakko? Maybe a thin blade under and slice them off.
That’s what I was thinking: use a good hobby knife (I don’t think I’d use a surgical scalpel — too fragile) to get into the seam between the upper deck and the stowage box. Be careful to keep your fingers away from where the blade will go if it slips, by the way. I once managed to stab myself
through my thumb because I wasn’t careful enough with something like this.
What did you glue them with? If it’s superglue then you can probably get the parts to pop off when the glue breaks, it being hard and somewhat brittle when cured; if you used liquid cement it’ll depend a lot on how much you used, though.
Another option if they won’t budge is to use a modelling saw, which will take off a bit more material. You can replace that with a bit of plastic strip, or you could just leave the boxes slightly lower than they should be, since it’s unlikely to be noticeable.
In any case, having the boxes on the right way is worth the bother, if you ask me. Leaving them like this doesn’t do the build any justice.