1. SugarCube waits until a Passage Transition (moving for one Passage to another) has occurred before it updates the History system with the current state (values) of the known Story Variables, this means any changes done to the story variables during the displaying of the current Passage aren't tracked by the History system and haven't happen as far as it's concerned. So if the page is refreshed then all the story variables changesmade while viewing the current Passage will be undo, and the same goes for any outcomes caused by the Reader selecting links that didn't result in a Passage Transition.
This is one reason why the 'end-less' page effect you're trying to implement isn't recommend if: it changes the values of story variables; or you want the selection of (non-transition) links to be remembered.
2. People can have different sized screens or web-broswer view-port than you, so if the new block of text being added is long then automatically scrolling downwards may cause the start of that new block of text to scroll off the top their screen.
Block of text...
<<linkreplace "blah blah">>
<<include "New Passage 2">>