This problem I faced after mistakenly deletion of my transformation file from project and while retrieving the file back in JDeveloper Project view. We can follow the same procedure for any other types of files present in BPEL Project.
1. Go to source of your BPEL project .jpr file
2. Search for the deleted file name
3. Delete the entries for <string v="-<<fileName>>"/>
4. close the project, refresh and check for the files in contents.
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