More stranger things: with the TP working, if I print its xinput properties, it says that the device is not enabled (even though it is working):
xinput list-props seeed-tp
Device 'seeed-tp':
Device Enabled (145): 0
[...]
Then, I can ‘break’ it touching the lower Y axis part, and it stops working, as always. BUT, I can enable it again, using:
xinput enable seeed-tp
xinput list-props seeed-tp
Device 'seeed-tp':
Device Enabled (145): 1
[...]
And then, it works again, and I can use the whole screen! 
It won’t stop working until the next reboot, when the device is disabled again. I need to check why is it disabled in the first instance, but at least, the problem is easy to workaround.
UPDATE: For those wondering, I ended up adding the following systemd service to fix the problem:
# cat /etc/systemd/system/xinput-enable-tp.service
[Unit]
Description=Run xinput to enable seeed-tp device
After=zynthian.service
[Service]
Environment=DISPLAY=:0
Environment=XAUTHORITY=/root/.Xauthority
Type=oneshot
ExecStart=/bin/bash -c 'while ! $(xset q > /dev/null 2>&1); do sleep 2; done; sleep 5; xinput enable seeed-tp'
RemainAfterExit=yes
[Install]
WantedBy=multi-user.target
It waits until Zynthian and Xorg are running, and then, after 5 seconds, it does the xinput trick. It’s not the most elegant solution, but as X is handled by Zynthian, and I don’t want to loose the hack on the next update, I couldn’t come up with a better solution 