1. Set up 2 separate portal instances, verify that both of them have the default Welcome page
2. Set up remote staging between them
3. Add pages testpage1, testpage2, testpage3 to the staging site at the same level as the Welcome page
4. Publish all pages to remote live, verify that they all got published properly
5. On the staging site, change something on testpage1, e.g. place an Asset Publisher on it
6. On the staging site, delete one of the other pages added in step 3. e.g. testpage3
7. Publish again, but select only testpage1 for publishing and check the "Delete missing pages" option
8. Check the pages on the live site
Result: The Welcome page also got deleted besides testpage3
The root cause is that the Welcome pages on the staging and remote sites have a different UUID but the same friendly URL (/home). The issue can also be reproduced with manually created pages that have different UUIDs but the same friendly URLs between the staging and live sites of remote staging.
This is currently blocked by another issue on trunk, but since the involved logic is the same, it should be affected.