Important to mention that FSX Repair ONLY affects default files, in default locations, so cannot help or effect aftermarket files in any way. This is only of concern if you have replacements for those default files - halo.bmp, texture folder, revised autogen files etc, etc.
What I have is a pure, clean vanilla install of FSX sited on a spare drive. I can pick and choose what gets replaced or overwritten. It's just as quick to create a virgin FSX installation as it is to repair the current one - just rename the current folder so that there's not confusion then install FSX and Acc into the same address. Rename the folder to `backup` and move it to the spare drive, rename the original folder to what it was before, and then copy/paste whatever you need.