Yes, ATF can remove your guns, even after all this time if they believe you've been guilty of a crime of domestic violence.
A domestic violence conviction will cost you your Federal gun rights. What's even worse is that under the Violence Against Women Act and the Lautenberg Amendment, the loss of your Federal rights is for life.
I know that you have said that your case was not labeled as a domestic violence matter. That is not relevant if the elements of your case conform to the Federal definition of a domestic violence case.
The Federal government defines a misdemeanor crime of domestic violence in 18 USC 1921:
"(A) Except as provided in subparagraph (C), the term misdemeanor crime of domestic violence means an offense that:
(i)is a misdemeanor under Federal, State, or Tribal law; and
(ii)has, as an element, the use or attempted use of physical force, or the threatened use of a deadly weapon, committed by a current or former spouse, parent, or guardian of the victim, by a person with whom the victim shares a child in common, by a person who is cohabiting with or has cohabited with the victim as a spouse, parent, or guardian, or by a person similarly situated to a spouse, parent, or guardian of the victim.
If your conviction conforms to the Federal definition of a crime of domestic violence, you have no Federal gun rights and, unfortunately, unless/until Federal law changes, you will not be able to acquire them again. However, if the facts of your convictio do not have the elements for a crime of domestic violence, then you can appeal this matter to the FBI.
Here's the form. There is a tremendous backlog on appeals thanks to recent toughening of gun laws. However, this is the only process available to those in your situation.