10/10/2016 at 4:54 pm #394955
If you have not altered the Connections plugin in any way, then you can safely deactivate and delete the current installed version and the reinstall from the Add Plugins admin page just like you did originally. The entries in the directory you have entered are safe and will not be deleted.
We’ll worry about the PHP notices only if they show after you update to a current version. However, per my previous advice you should disable the PHP notices if this is a live production site be cause it can be a security risk.