Importing directly from the assetstore/updater is fine for a new project.
but
NEVER on a existing project.
I highly recommend staying with the version of the assets you start your project with, also the engine version. Unless the update really adds something you
must have or need.
If you decide to just update everything continuously as they are released,
then do it like I do (the safe(r) way)
1) Always backup your project
2) Have a "blank" project where you import new assets
3) Then via files manager copy the asset from the blank to your current project.
This will give you the updated files, and not the install changes that comes
with importing some assets..
I even made a video on the subject!
On the lost configuration files matter, I'm afried you have to restore a to
the version you had before you started the download.