I've attempted to store a base64 encoded exe within a batch file, then use certutil -decode to turn it back into an EXE. I've followed the first answer on this question to achieve this: Store a file inside of a batch file? but despite the newly created EXE being exactly the same size as the original EXE, it doesn't run, at all.
I've noticed the Language property (right click the EXE then view properties > details) is not there on the newly created EXE. Would this be what's preventing it from executing? When attempting to execute the nely created EXE, a popup appears saying 'This app can't run on your PC'.
Use this command and you will see any differences that are there.
If it is not identical then the bat-2-exe converter isn't doing the conversion correctly.