If I upgrade from WSL1 to WSL2 will I still be able to access the filesystem in WSL1?
Yes; The upgrade process is seamless. However, performing a proper backup of your files, is key to any procedure like this.
I have a number of projects in WSL1 and also various virtual environments and environment variables set up in WSL1.
You should backup your projects in the event the upgrade process fails and makes the instance inaccessible.
I'm wondering if I will have to start from scratch in WSL2?
No; You can actually seamless transition between the two versions