If you vsix file contains a file that starts its name with a ".", then that file may get lost when repackaging your vsix file. In that case publishing the extension will fail with a cryptic error message:
error: Failed Request: Bad Request(400) - Specified part does not exist in the package.
tfx failed with error: Error: D:\a\r1\a\node_modules\.bin\tfx.cmd failed with return code: 4294967295