I can emphasize with both sides.
I don’t know what your friend does or the type of business he works for. Perhaps it is the type of business where the frum owner doesn’t make much money either since very few people conduct this type of business on yom tov or chol hamoed and the owner can’t afford to pay employees when the business is not operational.
On the other hand, not getting paid for 2 weeks is not an easy thing to deal with either.
Has this employee spoken with the employer about their Rosh Hashana agreement and why the terms were changed?