This started to be a problem around FPBX 2.8ish-2.9. Now it looks like you guys are doing more symlinking which causes more problems.
This shows up when someone installs Asterisk with make samples. Then freePBX cannot create symlinks because the files already exist. However, if someone installs Asterisk without make samples that causes other problems starting safe_asterisk and then installing freepbx. So the default for a lot of people (or at least for me) is to install with Asterisk make samples then install freepbx and let freepbx overwrite the samples.
But now that FreePBX is creating symlinks it's not smart enough to rename existing files or overwriting them so it just fails and I have to manually go in and delete or rename those files.
It would be great if FreePBX was smart enough to know that if there is an existing file the same as a symlink it is trying to create that it should rename that file. Just like how yum works where it creates a .new file of an existing .conf file before overwriting it or instead of.