I have a ProE assembly checked-in to Windchill and it has a corresponsing Windchill strucutre. When the ProE assembly is checked in 1st time then the corresponding Windchill structure is correct and all the WTParts are present in the structure. Now when some operation is performed on the assembly in Windchill for ex. check-out, check-in, change the state of the assembly etc then some of the parts from the Windchill structure go missing.
When we corrected the Windchill structure in Product Structure Explorer then the structure was correct but again performing some action as stated above made the same parts go missing from the Structure.
As per my understanding, you have checked in a proe assembly and auto-created WTParts along with it. After that, you have perform Checkin/Checkout from on WTParts from Browser and found that the Product structure does not shows some WTParts.