The EA is correct about filing as a sole proprietor.
Because you filed a Form 1065 for 2018, it would be best to file a Form 8832 to make sure that your choice is processed by the IRS. In Part I, line 6, you can select option c, A domestic eligible entity with a single owner electing to be disregarded as a separate entity.
In your letter, it would be best to point out that you didn't realize that an LLC owned by spouses is allowed to file a as sole proprietorship.
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