Yes there is but it might be better to track down the ctd. I recently went through this with one of my installs (FCOM again) and it was about reducing load order and removing mods that just aren't working - even though they did previously. You'd be surprised how creating a few test saves in an isolated cell and the deactivating mods and doing cell resets - you can identify what mods are causing the ctds - a large step toward either looking at fixing them or removing them.
But a reinstall? Why? it will be the same files and resources put back in. You could delete your ini and see if that helps when the game generates a new one.
Still to answer your question - when you uninstall it will only remove what was placed with the original install. So if you uninstall and then reinstall it will place the files back to where they were.
But again other than an ini setting that may be bad - it is doubtful your problems are due to the vanilla game - more likely a mod issue. And keeping all modded material will not solve that.