No, you will not need to amend your return related to this EIN on your LLC's 1099-MISC.
Since your LLC is considered a disregarded entity for federal income tax purposes, you will report this 1099-MISC income on Schedule C under your SSN. The IRS knows that disregarded LLC's income and expense amounts will be reported this way so having an EIN for the LLC on your 1099-MISC will not be an issue.
Just keep a copy of your 1099-MISC with your tax files for future reference.
