We've gotten this question several times already and it's a good question, so here's a page to describe some options.
The basic problem is that users looking to upgrade from V2 to V3 want to be able to transfer their old chip settings over to the new setup. There are two issues with this.
First, the new V3 application does not read V2 datalogs or V2 .ecu files. So you have no way to load up the old settings in the new application.
Second, even if the new V3 application did load those files, you still can't save the settings to the new V3 device because nearly every internal configuration record changed in some way with the V3 release. So doing a “Load from disk” followed by a “save all to ECU” would simply be impossible anyway.
After you've installed the V3 device in your, the first option for transferring old settings over would be to load up your old files in the old V2 application while you're connected to the car with the new V3 application and just copy over the tables one by one. That's a little difficult because the two screens are totally different and the V2 application requires that you constantly close and reopen various dialogs to do this.
But, it's an option you have available to you.
If possible, you should consider downloading the new V3 application before sending in your V2 setup to be upgraded. If you do so, you can connect to your V2 ECU using the new V3 application and save off the settings that way. Then, when you get V3 installed in the car, you can simply load up the old settings in one tab and connect to the ECU in another tab and manually transfer the configuration over.
Even with Option 2 above, you need to be careful about transferring the fuel, timing, airflow and VE tables over from V2 to V3 simply because the indices are different! In V3, fuel, timing and VE tables are indexed from 2000-10000 RPM. In V2, it was 0-8000. So you can't simply copy point by point. You have to shift the curve to the left when going from a V2 tab to a V3 tab.
Things are even more different with the airflow tab because the entire table structure is different! The best thing to do there is to copy over the points that you have a direct mapping for from V2 to V3 and then “smooth” the curve between those two points yourself in the V3 tab.