Flexi is built specially for one gallery at a time but this doesn't mean you cannot include multiple gallery on same page.
If you are using shortcode then just add a parameter clear="true" into it. It will deactivate the navigation and add unique identity to the each gallery and popup.
Gallery of album 1
[flexi-gallery clear="true" album="album_1"]
Gallery of album 2
[flexi-gallery clear="true" album="album_2"]
Gutenblock Builder (Visual Builder)
Since block builder is GUI based and shortcode is automatically generated at background you cannot add clear="true" to it. Hence there is a tool which need to be enabled.