Deactivating Vimeotheque PRO will cause you to lose all video embedding for regular post type or other custom post type that you implemented; the actual posts will still be visible but there will be no embedding.
Additionally, you will lose all PRO features, like automatic imports, private entities import (Vimeo folders, private showcases and private videos) or global embedding options. All PRO settings displayed in plugin Settings page will also be gone.
By deactivating the free Vimeotheque plugin, you will lose all video posts having custom post type vimeo-video (posts won’t be visible anymore); you will also lose all shortcode embeds made in regular posts or other post types or pages.
By re-activating the free version of Vimeotheque, all custom post type vimeo-video posts will be back and videos will be embedded in posts.