Let me check if I understand correctly:
1. You have a 4.0 site that works correctly.
2. You upgrade to 4.0 SP1 - it still works correctly.
3. If you change something in a template, some content is lost in the pages that use the template.
Is this the case?
If yes, can you send me a backup that I can restore to test this issue? I will need credentials to login as admin, and all custom master pages and themes, if you use any. It would be best if you can send me a backup that works correctly and is upgraded to SP1 and tell me which template you change to experience the issue. This will minimize the actions on my side to reproduce the problem which will ensure the test case is as close to your real environment as possible.
What was the problem:
The problem that we fixed is that when you published a template its controls got recreated, thus the placeholders received new IDs. Since the controls in the pages remember the IDs of their placeholder, they were not rendered - remembered IDs were the old IDs - those before the publishing of the template. This was spotted and fixed very quickly and there is a fix available in an internal build prior to 4.0 SP1. It should not happen, so I think that this is some different issue.
the Telerik team