While I should have expected this, it wasn't a huge deal since I just restarted my world (lost about 30 speed/energy upgrades). If you are upgrading to Mekanism v8, pull your upgrades out of your factories before restarting to update the mod. You can thank me later. :)

As far as fixing this issue? Not sure you can, but it should be reflected in the Upgrading to Mekanism v8 wiki page. 👍

This is part of the known consequences of updating - as you stated, pulling them out first will allow you to convert without loss.