What solved this for me was, in the product page I had multiple conditions and I had "All Conditions" chosen instead of "Any Condition". So unless I had all the conditions met on my product, it would not show in the collection linked. With Any, I can use whatever tag or type that I have set and it will show. Hope this helps, as I was not able to find this one as an answer. I luckily realized afterward that was the problem and sure enough it was.
I had the same issue and couldn't find a fix but I managed to do this and get it to work.
The products were all saying available on their own product pages but if I went into the bulk editor and selected the field "Available To Online Shop" they were all unticked. Once I ticked them, they started showing up again.
Not sure why the whole collection became unavailable after being fine and untouched for 2 months, but atleast its working now.
Hope this helps someone else.