There is no separate patch available at Humble.
At least I didn't see one.
But I don't know whether you can patch through the game itself.
I just logged into Humble and the only download for Eyes of Ara I found was for
the patched version of the full game --> TheEyesOfAra_1003_win.zip
TheEyesOfAra_1003_win.zip is 481.6 MB
slightly larger than the previous version, which was
TheEyesOfAra_1002_win.zip and was 476.8 MB
I went back and this time looked at the game itself and found a button labelled "Update" so I clicked on it .... Which started a "spinning" icon.
Did it ever finish spinning or give any indication of success?
If it did, I'd assume it's fine.