What flush_rewrite_rules(); does is call $wp_rewrite->flush_rules(); (Also called when updating permalinks).
All plugins rewrite rules are regenerated then, so you dont need to worry about other plugins rules being “missing”.
Also is not a good idea to call this function (flush_rewrite_rule) on hooks that run each time wordpress is loaded, and is enough to call add_rewrite_endpoint or add_rewrite_rule on activation or deactivation hooks.
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