The .htaccess file is being replaced by wordpress when you have settings in wp that htaccess. I had the same problem the first time I made changes to the .htaccess file. My quick fix was that I copied the setting in the htaccess file, then deleted it, and created a new .htaccess file while giving permissions only for the user/owner (me).
I then pasted the settings I had in the old one, and added some of my own.
The downside is, that wp can’t write to the file anymore, so if you make changes which require htaccess, they won’t work.
There must be a better solution to this, but I was in a rush, and that worked for me.