.htaccess is a dotfile which essentially means a hidden file. It seems that this is a recent file manager update where these files are no longer shown (But still there).
This is probably a bug because there ought to be a setting where you can display these files again.
In the meanwhile please use a desktop FTP client like FileZilla.
Iām sorry for the delay. It appears that there was an issue that resolved in files starting with a dot not being shown in the file manager, which includes the .htaccess file.
That has now been corrected, so you should see your .htaccess file again.