The e-filed return that included your original Injured Spouse Allocation form will be processed. What happens to the refund depends on how you made the allocations on Part III of Form 8379.
You're allowed to file Form 8379 on its own after you've filed your original return, just as you've done. See How To File in the Instructions for Form 8379. The Form 8379 you mailed should be processed, but you may receive correspondence from the IRS if you didn't include an adequate explanation of why you've filed it.
You don’t want to file an amended return. You only want to file Form 8379 with Form 1040-X (that is, an amended return) to claim a joint refund.
You might reach out to the IRS so that an assistor can leave a note on your account about what's happened. For telephone assistance, see Telephone and Local Assistance at the IRS' Let Us Help You page.