Did some more tests and here is what does and doesn't work for me.
Losing footage -
Yes I was having the issue (and the topic is in the premiere forum also)
Here is what seems to solve it.
It loses the footage if I use the original folder which has spaces in the name. Not sure if that is the culprit but both methods proved consistent in every test I did.
it worked when I used a new folder called "Test" at the root of my editing drive.
Not sure if other have the issue but when I close AE, PPro will just sit there with an hour glass and show as not responding.
If I close PPro first and then AE and reopen PPro then all seems to work as it is supposed to.