If a content owner deactivates a reference file, it will:

When a content owner deactivates a reference file, YouTube's Content ID system will cease to claim new user-uploaded content that matches that specific reference file. This action effectively stops the automatic claiming process for future uploads. It does not release prior claims, which remain active unless manually released. Deactivation also doesn't involve a temporary suspension or a change in match policy; it simply halts the claiming of new matches. Therefore, the primary effect is to prevent new claims based on that deactivated reference file.