Sorry to refer to some of the older posts. I think my case was somewhat related.

I had a problem 2 weeks ago, and wonder if anyone could help, so I would not have to deal with this again in the future. I will try to be concise, but please bear with me.

Original itinerary: PHL AA x/BOS AA x/JFK AA*/JL x/HND JL TSA, all on 1 ticket (AA-001 stock). The JFK-HND flight is AA-marketed and JL-operated. TSA, for those who don't know, is the smaller airport in TPE.

Transits in both BOS and JFK are 2~3 hours, but the one in HND is 16 hours and overnight (which is allowed airside). I departed from PHL on 18APR. The JFK-HND flight also departed on 18APR but arrived on 19APR, and the HND-TSA flight departed on 20APR.

I was able to do online check-in for all 4 flights (got all the PDF boarding passes) on 17APR on AA.com. When I went to PHL airport, I first tried the kiosk (just to see how far I could get). The kiosk only wanted to check me to HND, so I went to the Priority counter. The agent first started to check my documents needed for travel and kept asking things that didn't make sense to me. It took quite a while before I realized she was asking for entry documents for Japan (MySOS App, etc.). I told her I was going to Taiwan, not Japan, and I would stay airside overnight at HND. She told me she could not change what her screen asked her to check. I did raise my voice to tell her she was looking at the wrong set of requirements, but her reply was if I kept yelling, she would call security. After some time, she did get her supervisor over, and the guy from another counter also came to help.

At the end (way beyond bag check cutoff time) they were okay with me not filling out the form in MySOS, as long as I downloaded the app. However, they insisted they could only check my bag to HND, because AA would not check a bag overnight, domestic or international. Throughout the process (mostly because their confusion of the documents I needed to enter Taiwan, not Japan), I repeatedly asked them to short-check to JFK and I would re-check with JL desk at JFK, and they refused. They told me to recheck my bag at HND, even though I told them I would not be able to go landside at HND. They then told me I had 12 minutes before the gate would close and would really need to get going. I agreed, did my best, but still missed the flight.

I went to the AC and had a much better interaction there. The agent rebooked me to PHL AA x/LAX CI TPE (involuntary re-routing, no charge). To my surprise, my bag actually made the PHL-BOS flight, but because I would be waiting in PHL for 9 hours, my bag was returned to PHL by the next BOS-PHL flight and flew with me back to TPE.

The AC AAngel told me to write the problem I faced to AA Customer Relations. I did and just got a meaningless reply. The first 40% of the reply was sorry and comments had been shared internally. The other 60% of the reply was how I should have joined AAdvantage for more benefits. Heck, I am a CX Sapphire member!

I had some time in LAX FL. Since they have flights to Asia (or used to have) and in fact Japanese AAngels there, I decided to ask them again how I could have gotten the check-in agent to override the questions on her screen and check my bags to TSA. The Japanese AAngels discussed among themselves, looked over several things, and discussed with another supervisor-looking person who popped up at the FL, but their conclusion was:
1. Changing the final destination from HND to TSA used to be doable on the native Sabre system, but not with the Qik overlay now.
2. Short-checking to JFK would have been the solution, but this is supervisor's discretion, and most supervisors would not do it.
3. AA's system cannot through check a bag if the flight's departure time is more than 24 hours from the check-in time. [This one I seriously doubt.]
They were trying to ask another check-in agent veteran for comments, but they could not get an answer before i had to leave for the CI flight. I asked if I could have their email so they could let me know if they find anything new, but they couldn't give me their email. They were confident Customer Relations would be able to resolve this. Oh well...

So, I'm currently stuck. I only have status with oneworld. Since I can only fly Y, having status benefits is quite important. CX is almost not operational these days. My only TPAC option is AA+JL. I have no problem going from Taiwan to North America, as same-day connections at NRT are available 2 days a week. Going back though, the only option would be an overnight transit at HND. There are simply no same-day options these days, and NRT closes at night. If AA's system does not support it, and Japan still has entry restrictions, I will be out of oneworld option if I need domestic AA flight(s) before the JL flight. I also have a hard time believing AA had not checked anyone over an HND overnight transit before.

Before I write back to AA Customer Relations, I would like to ask if anyone knows of a way (refer to certain STAR file, etc.) to:
1) Have a bag checked overnight in a foreign transit point (HND in my case, but certainly there are people who do it at DOH, HKG, etc.?)
2) Have the agent add 1 more flight to the check-in list, so the system would ask for the documents for the correct final destination

I also wonder, how come AA's system had no problem checking me in online to TSA, but eventually recognized my final destination as HND by the time I got to the airport. I hope my playing with the kiosk did not change this.

Note: I did YQB AC x/YUL AC x/ORD JL x/HND JL TSA a few months ago, with very similarly timed flights (overnight transit at HND as well, and the HND-TSA flight was also 2 calendar days after), and the AC check-in agent at YQB had no problem with either document check or bag through-check.