I published a package successfully but I do not see any (or some of the) files I expected.
When you add a file to eB, the "signature" of the file (i.e. its file size anfd hash key) is stored in a table. When you access the file (e.g. view, launch, checkout, publish etc.) eB will make sure the file currently in the repository matches the stored signature, before presenting it to the calling process/functionality. For example if you launch a file that does not match its signature, which might have been a result of transmission errors, unauthorized repository substitutions or other ways the file might get corrupted, eB will display an error about the signature mismatch.
In the case of Publisher, these signature mismatched files will just get ignored, meaning they will not be downloaded/exported to the destination folder. The solution is to fix these files first (via a file repair job or from a known good backup) before attempting the publishing action.