This really seems to be an issue that Amtrak would control, since you voluntarily transferred the points/miles there.
I miss the good old days when you could go directly from AMEX to AA. At this point, there is really nothing in the current problem that affects AA. It seems like you are referring to being stuck getting the points from Amtrak to Choice.

Your post should serve as a warning, before doing these kinds of transfers. make sure you can do it (under the T&Cs of all programs involved), before you actually attempt to do it.