I think it would help if you indicated whether you are on PC or gamepad.

I have been experiencing a similar issue with hotbars, but I am on gamepad.

My hotbars retain their non-macro skills and menus. But the macros I put on certain spots are sometimes swapped out with another macro.

For example, my WHM has a macro for using Eye for an Eye that lets the party know it has been applied to someone.

Today upon first time logging in, I found that it has been replaced with a Blood for Blood macro I had also made for other jobs.