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Because every time I edit a link in "SEF URLs", it breaks the links that I copy/pasted from my top menu on the frontend.
That's expected, sh404SEF does not use menu items to build URLs. URLs - at least for Joomla standard content - are created based on the items themselves, their categories, etc, not based on how the item was navigated to from the menu.
What is the best link/URL to use so even if I edit the "SEF URLs" section, it will not break links? and how do I find that link?
The standard way to insert links with Joomla is to use the non-sef version. That's the link that will always work. Joomla will detect those links if they start with "index.php?...." and convert them automatically to SEF URLs.
Using non-sef is the future proof way. If you use SEF links directly, and you have to change them at some point - which should be avoided of course, you'll have to redo all the links or add redirects, etc.
and how do I find that link?
I have found that simply using the JCE editor and insert links from it works the best. It shows you the available content for linking and inserts the proper non-sef links.
To note, I have to "Purge" after each time after I edit a link in "SEF URLs" for my menu item links to work again, is this normal?
You should never Purge - after the initial set up of sh404SEF.
If you use menu links as you described initially, they are supposed to not work.