You must make sure that the VERSIONS are compatible. Don't install files for 1.3.8 if your DB is 1.3.6.
But if you load up FILES of the same version it should be fine.
Re-install your database and point the two configure.php files to it.
There are likely to be some issues (blank pages most probably) until you get your files set up to dovetail with the database. This will happen, for example, if/when the php references the database for the template you originally used - and can't find it... Revert to "CLASSIC" for the time being...
Aslo, if you installed additional modules you'll get errors.
As I said, in most cases, these are because there are settings in your database that rely on what you did in the original PHP. When you get an error, note it down and think about WHY that error is appearing... You'll find yourself saying... Oh yes... that's because I had XYZ module before...
... go get that module and re-upload it to your store.
Eventually, it will come right.