2 LE installations in two folders

I’m on a managed root server running on FreeBSD. I had installed LE as a git clone as described in the doc. Running LE didn’t work and a message informed me that FreeBSD is still not fully supported. It suggested to install “pkg install py27-letsencrypt”, which I did.
However, a few days later, the hosting company installed LE as part of their managed root update. I now have a LE installation at
"/home/admin/letsencrypt/" and at

The good thing is that it works.
But I don’t really like to have those two installations. How can I delete the git clone that I had installed myself? Would this be safe to do?