I switched to Storefront – the same problem. After activation “regenerate product lookup tables” native WP filters widgets work several mins and after that all filters disappear from shop page.
No any scheduled actions at woocoomerce status tab, regeneration task is completed.
I guess the issue is WooCoomerce 6.3.x
I took a decision to move back to WooCoomerce 6.2.2 and wait for new woocommerce release. WooCoomerce 6.2.2 – no any problem at all.
No any modification done with woodmart theme, only native settings.