Encoded packages should work in the Wolfram Cloud, and on seeing your question, I have successfully uploaded an encoded pacakge and loaded it with Get[filename, key].
I wonder if the package is uploaded successfully. You could try FileHash[filename, "MD5"] on both desktop and in cloud and compare the hashes to check that.
Short of that, you could post discrete steps you tried, maybe myself or someone here could spot where it's going wrong or suggest further diagnostic steps.