Ouch!
It would depend greatly on exactly what the "burr" looks like and how it got there. If it is entirely in the window, and has not disturbed the bore, then I would try in this order of preference: X-acto, Swiss needle file(s), slipstone, and only as a very last resort a Dremel with a stone.
On some chromed liners, there would be chrome "nuggets" left in the windows that might break off and ruin the engine when running. This might be an example of something that needed attention prior to running. I have seen this on a few GZ engines and cleaned up with the X-acto.
If the "burr" was created by a broken ring during assembly/disassembly/running, then it is likely that metal was moved into the bore. Since metal does not compress, a ding in one place guarantees a bump somewhere else. One way to try to check this is to take a gauge pin (or drill blank) and roll it around inside the bore. Roll it over the suspected area. If you can feel any rocking top to bottom then you have a problem. Even if you can't, you may still have a problem.
It would take a lot to convince me that a hone (like a 3-stone spring mounted unit) would take care of a local bump without grinding away material in places you don't want ground away. A hone is not a reshaping tool. It is a "knock down the tool marks" tool. I always worry that an abused--or just well used--hone has stones that are no longer flat. (Not really flat in two axes, but straight along the rotation axis.) Again, you would be taking off material in places that you don't really want to. Making a bore wavy while trying to remove a burr is not an improvement.
If you know someone with a Sunnen hone, who has the tooling and knows how to use it that would seem to be a good prospect. Then find out how much. Likely that custom work is more than a replacement part. The real dilemma here is attempting a rude fix, then running it to see if it all worked out, and then ruining the piston, ring, head, plug and whatever else gets pounded with shrapnel.
It would take a very deft touch with a Dremel to clean up a local spot, but would be better than attempting a hone on the cylinder in my opinion if a significant ding protrudes into the bore. Perhaps best would be an adjustable lap than you could attempt to localize to the area in question. Again, not a great bet. You have the advantage of going slow with a lap.
The old shampoo/conditioner advertisement from way back had it right: Just Don't Do The Damage In The First Place.
I know, not very helpful after the fact.
Sorry to hear of your troubles,
Dave