Hi,
UpdraftPlus doesn’t have any code for writing to the .htaccess file…. so you’ll need to look for other culprits… do you have any security-related plugins that put stuff in this file? (I guess the obvious ones to look at would be look at would be any that are writing to the file… what’s in the file normally, and what’s in it when it’s messed up?).
The only way I can see that UpdraftPlus would write to it is if you’ve reconfigured the directory that UpdraftPlus uses for its backups to be the same directory as the root of your WP site (this setting is in the ‘expert’ section of the UD settings tab). Don’t do that, if so… go in there, and check that you’ve got something set in there, or reset it to the default if it’s been emptied by some other method (there’s a link for that).
Best wishes,
David