I've had similar experiences. I tend to make backups of my profile directory now which seems to fix it once I rewrite to it. Here's some helpful tips: Always make a backup of the macro file in the folder
swggalaxies/profiles/YourUserAccountName/macros.txt so if it gets wiped you can easily replace it.
Use
load txt.files for long macros then in your hotbutton macro you only have to load the command to activate it. This is a whole lot easier (especially to edit them) then using long macros in the in-game macros itself.
More info on macros can be found
here.
Edited, Thu Jan 8 13:11:24 2004 by VicVega