Let me try answering questions for you:
Can 1000 Configuration file be directly imported into 3000 Series controller?
Yes, you can apply ZD1000 backup configuration file into ZD3000 however it is not possible other way round. I mean from Zd3000 to ZD1000 or ZD1100.
Please note and is important that when you go this lane then make sure whatever firmware version ZD1000 backup configuration file it is, same should be loaded on Zd3000.
Let say you pulled ZD1000 backup configuration file at the time ZD1000 was running X firmware version, same version shall be running on Zd3000 at the time of applying this file.
As far as migration is concerned, Once my ZD3000 is ready to be put into network and Zd1000 removed. I will make sure all AP's are knowing the one zd IP address so once you disconnect ZD1000 and zd3000 is brought online, ZD3000 will have same old IP as Zd1000. At any point of time, only one ZD is live. All APs will reconnect back to ZD3000.
I hope this helps.