Currently, there's no way to exclude specific numbers from the "Remove Bad Numbers" process. If you choose to remove all bad numbers, it will remove all numbers identified as bad from your selected group.
Workaround:
If you know a number is valid or will be valid soon, you can add it back to your contact group after the removal process is complete.
Here's how:
Remove bad numbers: Follow the steps in the "Using the Bad Numbers Removal Tool" article to remove invalid numbers from your group.
Add the valid number back: After the removal is done, manually add the valid number back into your group. You can find instructions on adding contacts in the "Managing Your Contact Groups" article (or similar).