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Hi! I have set third binding on 88 port, and an according webserver works as expected. Unfortunately, Let's Encrypt did not renewed authorization tonight — could not write its file to .well-known/acme-challenge/

Not a big problem, I have renewed its certificate manually via an ordinary binding, and then switched it back to 88.

However, would there some way to let LE access this website over a non-standard port?

You could use the Linux firewall to redirect traffic from the LE CA server to the other port.