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Well, just as I suspected, the problem with writing to the SD card was totally caused by me . It all works perfectly now. Just need to treat it with care. I implemented a Queue which everything writes to, then a dedicated SD card thread simply processes that queue at its leisure at regular intervals.
Having everything try to write to the SD card (even in different files) just like it always worked on desktop hard disks just didn't give the sort of reliable results that I could feel comfortable with.
Quite a few times I mistakenly connected RX pin to RX of USB-TTL cable (and TX to TX)... even when there was stuff that was supposed to be sent/received over the cable (until I figured out why it was not working!). Never had an issue.