I am having a problem working with UserProfileManager.GetChanges, it seems that it has a limit of 1000, can anyone verify this? And what is the possible way to increase the cap? There seems to be lacking documentation for this on http://msdn.microsoft.com/en-us/library/office/Microsoft.Office.Server.UserProfiles.UserProfileManager.GetChanges(v=office.15).aspx
If you look at the internals of the GetChanges method, it calls a stored procedure dbo.profile_GetUserEvents which returns 1000 records. Another option appears to be to add a query to the GetChanges method. Within the query there is the option of setting a ChangeTokenStart property with a date. You can try that method.
This seems be some issue with the object model that there is no way specified or documented anywhere to get more than 1000 changes.