I have seen this raised a few times as an issue, but this is standard behaviour and by design. This post will show you how this warning is replicated. For those of you that haven’t seen this warning before it states:
Project Out of Sync: Resources or Calendars have been changed and will be updated on your next save. To update your project now, click Sync
As the message suggests, this warning is given because either one of the Resources or Calendars have been edited since the Project was last saved. If you want to see the effect of the change straightaway click Sync otherwise all will update when the project is modified and saved. To demonstrate how this warning is replicated see the steps below.
In the example above I have two resources, for the purpose of this example I will now edit the standard rate of UserA from £20 /h to £30 /h (I wont show how to do this!). Then open the project in the web, in this example it is Project1
Now click Edit > In Project Web App and you will see the Project Out of Sync warning:
As mentioned earlier you can either click Sync to update the plan with the new Resource cost or this will update when making changes to the project and saving.
Hope that saves some confusion