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Whatever you do on one partition will not affect the other partitions. I would not recommend that you run Fdisk except to look at partition *information* - just format what you need to wipe. Whenever you restore an old registry, you will lose *access* to anything you have installed since that registry - you will have to reinstall it - but you will not lose any data.
If you are in the habit of installing things frequently that you are not sure about their compatibility or safety, reboot to DOS and run SCANREG/BACKUP and reboot before trying to install anything that may be risky. You could also consider using GoBack and running a restore point before doing anything risky.
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