Update:

My onion2+ uses a 1GB sd card as a root overlay.

for some unknown reason, 3 "invalid encoding" files with zero byte length are written on the root fs, "/". I have no idea what process creates these 3 files.

When these these files are present they interfere with /dev/ttyS1 communications and affect both python scripts and avrude write operations to the arduino dock2.

to correct this problem, I remove the SD card from the onion, fsck it in a laptop, (which is clean, without issue), and use nautilus to delete the 3 files from the SD card.

Restarting the onion with the files removed, serial communications to /dev/ttyS1 returns to normal.