No, you won't.

During the activation of your Auto-Align 2 upgrade license using the iLok License Manager, you'll be asked to surrender your Auto-Align 1 license.
After you complete the surrendering process, a group license will be deposited to your iLok account.
This group license includes Auto-Align 1 and Auto-Align 2 licenses.

The group license allows up to 2 activations. You can activate your license on your machine and/or iLok device.
Your old projects with Auto-Align (1) will open with no issues.