In the latest version of NodeCanvas there is an new feature added to optionally serialize the graph asset to an external text file, which was added exactly for these situations and for better source control (git) support. (This is still undocumented but will do so soon).
To enable this, select the graph asset you want, then in its inspector click the “Create External Serialization Text Asset” button. This will prompt you to create a text asset and the graph will from now on serialize to and deserialize from that text asset (in addition to within itself) as long as the text asset is still assigned. The json in that text asset is in pretty format and therefore better suited for source control.