BPS comes with pre-made root and wp-admin htaccess files. So if you are not using those BPS htaccess files and the code is different in the restored htaccess file then it is very likely the cause of why this odd problem occurred. BPS is designed to work with BPS htaccess files, but you can also create your own custom htaccess files and code. You just need to make sure your custom htaccess code/files are good/valid.
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