Supposedly you can have cfg tweaks and it will work fine, its just modified dlls and textures that can cause an issue. Although they say the cfg tweaks from before are no longer useful after SP1. If you deleted the cfg FSX will build a new one.
Here's more info from the devs:
FSX SP1:Preparing to Install
Setting up for SP1
SP1 needs a pristine RTM.
That includes no add-ons. Many 3rd party add-ons can cause crashes, especially if they load dlls. In that case they will likely need to be refreshed.
If you really don’t want to do this, then perhaps you can consider running FSX from the command line using
This provides a dialog for every dll or xml exe that gets loaded so you track down who is the offender if there is an issue.
However, most people don’t know how to run FSX from the command line, thus it’s safest to uninstall all add-ons.
If you have performed any file modification tweaks, you will need to uninstall or repair RTM.
Then install SP1.
Then start installing your add-ons 1 by 1.
Uninstalling RTM deletes ALL content of -
C:\Documents and Settings\All Users\Application Data\Microsoft\FSX
C:\Documents and Settings\USERNAME\Application Data\Microsoft\FSX
That is EVERY subfolder & file in that branch.
If you don't back up and save, you will loose config files, flights, logbook, and rewards.
Two files to consider saving:
FSInsider.com will have an article live that discusses the uninstall scenario in more depth, please take the time to read it.