Unless this has been addressed in proe versions more recent than wf1, the only way to deal with this problemis to open the assemblymodel and search for the missing parts in resolve mode. The failure diagnostic gives the name of the missing file, however, if you have changed the name of the file you should be able to select it using its new name (provided that you have not changed the references in the component). The assembly should finish regenerating correctly afterwards. If you have many parts in your assembly with this problem, you will have to repeat this for each one. I submitted an enhancement request to ptc about this over a year ago. Perhaps, if it is a serious problem for you, you might consider doing the same so that they can see that customers would value this feature.
Also, I might add that you shouldmake sure that when you rename a part that is a component in an assembly, you must make sure that the assembly is in session. After you rename the part, you must then save the assembly. This will ensure that the next time you open the assembly it will load the newly renamed part. This applies to parts in drawings, and parts withmerged or inherited models as well.
You can do a search in Windoze explorer for files named *.drw.* and *.asm.* containing the text string of the model name. This can take a very long time if you have a lot of files. The best solution is to use a PDM system to manage your data. The second best solution is to not rename Pro/E files! This is not a bug and you are not going to see any change in this behavior. PTC have a solution, it is called Interlink.
Yup rmkinley is right to stress out that when you rename a part which is a component from an assembly that assembly must be in session and then you must save the assembly after the renaming. This may help in the sorting of your assemblies, make a directory for every subassembly so you have a back-up.