I was having this same problem. I placed a subassembly inside my final .iam. I needed to animate the original constraints from the subassembly while in the final .iam. When I clicked on the plus sign next to the subassembly in the project browser, I did not see all of the parts that were in the subassembly. All I saw were the representations and origins folders. Turns out I had set the project browser filter to "Show Children Only." All you need to do to fix this is click on the filter icon just above the project browser, and uncheck Show Children Only. Then all of the individual .ipts should show back up in your project browser.