Nothing is stopping you. After the form is approved you can send a letter to ATF saying that the caliber is now 9mm. When you want to go back, you can send another letter. Most people do not even bother with the letter since there is no duty to report even the removal of a weapon from SBR configuration.
If you want to have 9mm on the form, you can file by paper. This is a current limitation on the eForm system.
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