I got that problem too, after some update i got the message that the website is not protected and i should create a new master .htaccess.
I did that and then got the message :
W3 Total Cache is activated, but W3TC htaccess code was NOT found in your root htaccess file.
W3TC needs to be redeployed by clicking either the W3TC …
I tried strep by step how you describe here, but it is still there.
How is that possible?
Where do i find the “W3TC caching code” which i can copy in the BPS Custom Code text box?
Kind Regards