We don't have all the details of your itinerary (the airlines/flights/times), but what is most likely in your situation is that your luggage will be checked-through to the final destination, and you will not see it in Frankfurt.
Contrary to what happens in some cases (like when you transit international-to-domestic in certain countries, or even international-to-international in the US), you don't see your bags at the port of entry into the EU. You will go through passport control there, but your bags are transferred through, and will go through customs in BER (customs officers can recognise bags which come from outside the EU because they don't have green borders on the tags).
What you want to do is "short-checking" of your luggage, so you can retrieve it before in Frankfurt instead of Berlin. If you have a flexible ticket this is usually not an issue, but for the less flexible (cheaper) tickets this is often not possible.
The reason why they won't allow it is because flights with many layovers are often sold at a discount compared to direct flights (or flights with fewer connections) on the same origin/destination or to individual legs of that route. So people try to do what is called "hidden city ticketing", buying a cheap A-B-C flight and then only using A-B, which is more expensive.
To them, that's what you are trying to do, and that's probably part of the reason for the cost: your ticket was repriced for the new (shorter but more expensive) itinerary, plus possibly change fees, plus possibly the fact that the prices on the itinerary went up as the flights filled up.
It so happens that in your case there are no flights from PNH to BER with less than 2 stops, very few shorter flights overall, and PNH-BKK-FRA is actually cheaper than PNH-BKK-FRA-BER (at least on the date I checked) but they don't necessarily apply rules on a case-by-case basis (way too many variables), and just apply a blanket policy.
I'm surprised that with the shorter itinerary being so much cheaper than the full one (at least on the date I randomly picked) you end up with such a large charge for the change, though.
You can always ask at check-in to have your bags short-checked to FRA, but the chances are low that it will happen, and you will only know at that time.
If you have a long layover in FRA (seems unlikely to me, there's nearly a flight per hour on that route) you may be able to ask to retrieve your bags there (supposedly to recheck them later), but since that would mean going through passport control, baggage claim, check-in and security (on the arrivals/departures path, not the connecting path) they would only do it (if at all) if there was ample time.
And not showing up for a flight would also lead to all further segments on the same ticket (including return flights, if any) to be cancelled.
I'm afraid the only options I can see you could rely on are:
- Not checking in any bags (carry-on only) and getting off in FRA (any further flights cancelled)
- Try to rebook on a different itinerary. The cost may be different the day before or after for instance, or on another route on the same alliance. Do NOT mention cancelling anything, just that you have a change in plans and want to rebook to a different destination. Look up prices for that itinerary before you call them to know the options and the relative prices (or see if you can make any changes online directly). Note that if this is a return flight, comparing current prices for the whole trip or just the return flights with the actual prices that would apply to your trip can be a complex exercise, but it will at least give you an idea of the relative cost of different options. You may need to read the detailed fare rules of your flight.
- If you are very lucky, you could change your flight to include a stopover (a long layover over 24 hours) in FRA, in which case you would indeed retrieve your bags. But not all fares allow it, and not necessarily at any connection airport (policies vary widely between airlines and fares).
- Keep to the original plan and travel back to FRA afterwards. You can try to ask for the luggage to be short-checked to FRA when you check-in, but you'll only know at that point. Again, any further flights would be cancelled if you pull that off.
Anything else is at the whim of the check-in agent and you won't know until the sticker is added to your bag.
