The definitions of "pistol" and "semi automatic assault rifle" are not limited by date of purchase, neither is the 9.41.139 mandate for continuing eligibility checks for persons who purchased a pistol or semi auto rifle pursuant to any provision of 9.41. A court might interpret this as I-594 and later.
The pistols they could maybe use the waiver on the old forms, but rifles no way. For one, you didn't sign a waiver when purchasing one prior to 1 Jul. Two, I'll stand by the definition of "acquired pursuant to this chapter" requires that the item existed at the time you acquired it. No one "acquired" a "semiautomatic assault rifle" prior to 1 Jul because they did didn't exist. You acquired a rifle. They can change the definition moving forward, but at the time of acquisition it was just a rifle.
The state can conduct a "background check" on whoever they want at any time, but accessing certain information (health records) requires either a release or a law enforcement exception. For rifles purchased prior to 1 Jul they have no release express or implied, and suspicionless blanket searches don't qualify for a law enforcement exception.