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I finally actually did some testing with my own board and managed to get most of the same errors you found in Bypass mode and pushed some corrections to TinyGSM. It’s all about the issues with synchronous and asynchronous opening. I figured out how to make it crash every time and (hopefully) how to make that not happen. And the good news is that since both the XBee3 in Bypass and the Sodaq UBee are using the same code in TinyGSM, it should help both of them.
As for the issues with not connecting in transparent.. I’ve got nothing. Try some prayers to Isidore of Seville, patron of the internet. Sometimes switching the same board back and forth between transparent and bypass mode a couple of times works. More often I’ve been able to “fix” a board that wouldn’t connect in transparent by using bypass, but today I had three different boards that I couldn’t get to connect in bypass and suddenly happily connected in transparent. I have no idea why it happens.