.htaccess has old w3tc directives

Yes, you should remove them, since the .htaccess file should contain minimal settings. Apache doesn’t play well with conflicting rules.

.htaccess rules are quite complicated, as you can tell by the sheer number of rewrite conditions WP Super Cache’s inserts when enabling caching via mod_rewrite, and thus those rules are very canonical in nature.

Simply put, an .htaccess file shouldn’t contain any rules that are absolutely not necessary, as they affect everything from page serving to how web crawlers and malware purposefully access and index your website. I recommend you delete them or at least comment them out by using the “#” character at the beginning of each line.