Can I return to Thailand on an education visa after obtaining a re-entry permit?

When your educational visa expires, ALL RIGHTS to re-enter Thailand under a re-entry permit EXPIRE with it.

I went away for 40 days last year, on my return the immigration officer asked basic questions in thai (name, school name etc) and why I left during classes.

I presented the immigration officer with the “letter of absence” which I got from school. Stating my reason for leaving country during classes and that I will be taking online lessons.

Very reluctantly they allowed me in.

While issuing the letter my school messaged me this

You may deny to enter Thailand.

1) If you cannot speak Thai.

2) If you leave the country many times, or longer than 2 weeks.

You may have difficulty re-entering after a period away on a Visa which requires you to attend classes. Be prepared at least for a grilling.

A re-entry permit wouldn't give you any additional days to your current stamp. It is only valid as same as your current stamp. If your current stamp expires when you want to go back to Thailand, a re-entry stamp does not do any trick.