I've been using Bash on Ubuntu on Windows since its been announced in beta and have tools installed, bashrc configurations, etc. From what I understand, its not really supported anymore and I have to move to the official store app for Canonical updates and support. What is a sure way routine of doing this without having the reinstall tools and packages?
As Ramhound mentioned, MS officially suggested migrating files to the new store-delivered instance (I guess the legary lxrun-installed instance will never receive 18.04 LTS or any later version). I have yet to do the migration, but I think the reasonable way of moving into new instance is like this:
Start sshd on the old instance:
sudo /usr/sbin/sshd -D
Run scp from the new instance:
scp -r localhost:~/* /tmp/- this will keep your file modes, while copying to a Windows filesystem will destroy them (setting everything to 0777)
sudo, the directory tree in the new instance with what you just copied.
Be sure that nothing is running in the background of WSL if you're going to replace system directories. You will need to copy /bin, /etc, /home, /opt, /sbin, /usr, and /var if you want a full recovery, but only doing
/usr/local (which contains libraries installed or compiled manually) and install repository packages again with
apt might be a safer option.