So for this it helps to understand what these commands are doing. Apache is pointing at these server.* files in this specific location, and what these commands are doing is replacing those with soft links to files that are somewhere else. That way Apache can continue to point to the original files, but what is actually served at those locations is your cert instead.
So the first three lines are just renaming (linux "mv" or move command) the original ones to .old just so we have them in case we need them. The other commands create soft links. When we're done, you can request the apache conf version of the file but what your'e really requesting is the lego jobay version of the file.
Lastly notice that you're renaming (moving) three files but only making two soft links. That's because some certificate managers need all three, but letsencrypt only needs two. We move server.csr but don't replace it with anything. Lots more info here: https://letsencrypt.org/how-it-works/
So 1) If this is your second time running through these steps you don't need to move the files, you've already done that. 2) The error that server.csr doesn't exist is totally expected. You moved it last time. 3) It looks kind of to me like you may have accidentally soft linked the .old files rather than the .crt and .key files, last time.
Run this command:
ls -l /opt/bitnami/apache2/conf/
Soft links are obvious, they show the file that's in the directory and then an arrow and the file that it's really pointed at. When this is done right you want
server.crt -> /path/to/jobay.crt and
server.key -> /path/to/jobay.key
If you have something else (bad or broken soft links) you're going to need to (carefully!)
sudo rm the soft links you do have and then run the
sudo ln -s commands again.
It's also possible, based on what you've posted so far, that all of these errors can be ignored; it looks like you may have already done what you needed to do, scary error messages aside.