The redirection feature of TSF is controlled via metadata only, which resaving of permalinks cannot affect directly.
Only when you’ve knowingly entered the homepage URL as a redirect URL in TSF’s meta fields, TSF could redirect a request to the homepage. In this case, when TSF redirects to the homepage when it isn’t expected, then another plugin tricked WordPress into loading the incorrect metadata, which TSF then executes. The issue lies solely with that plugin.
When you haven’t entered a redirect to the homepage in TSF’s fields, it can definitely not be an issue of TSF. The issue lies elsewhere, for TSF no longer interacts with the Rewrite API since version 4.0 (September 2019).
1. Some plugins resave permalinks when you (de)activate any plugin, which makes it seem TSF is the culprit, while it is another plugin’s mistake. This is incredibly difficult to debug, so that’s why we took our hands from this system.
2. Some plugins register Rewrite Rules incorrectly, which causes some endpoints to disappear… almost at random because they may interact with the API on specific queries only or otherwise in the wrong order. Either case is against guidelines and causes sporadic behavior in WordPress. This, too, is incredibly difficult to debug, so that’s why we… you know the story.
3. Some hosting parties have incorrectly set up NGINX, causing it not to consider (or even overtake) some specific sequences of rewrite rules. This, again, is incredibly difficult to debug…
4. .htaccess of Apache may too overwrite rewrite rules. However, if you only notice these issues infrequently, then it is again this debug thing that’s incredibly difficult to do…
I could go on with this list forever… this point is that it’s difficult to debug, and it’s best to hire a developer skilled with the WordPress Rewrite API.
If you firmly believe the issue lies with TSF, please do follow up. Thanks!