Hello. Our script only opens files that your after installation can open and saves for the current version. It just automates the process to do it in batch.
If you have to convert a lot of very old files (version 6.0 and earlier) you need to use the CS6 version of after effects. Because it can open these very old files. It's the only way for now.
We have plans to develop a tool to downgrade the version of AEP files. But not for this year.