FacetWP had introduced WP-CLI interface which I was very much looking for. Just run
wp facetwp index and reindex for the entire site will be created.
I just had a moment in one of my online stores where I saw that the index was last built 8 months ago. Now can add this line to WP All Import bash script and index will be built quickly every time. Or run it once day for example together with daily backup. I find it very convenient.