Hi @thehiggman​ ,

I encountered a similar issue recently and here's how I got my connections working again.

At our organization we have a shared folder that contains various connection files (ArcGIS SDE connection files, vendor specific connections, etc.) .

What I had to do was update my Default Paths to the shared location in FME Options.

Tools --> FME Options --> Default Paths

Once here I updated my Data Path and Public File Key File.