Have a look to this KB:
Point 7 says you can exclude the shared objects between source and target from the deployment group.
In your case I don't know if your shared objects are carrying changes too.
If you are using same shared objects in both the groups then it might get affected after you perform the second deployment.
You can keep the objects isolated in two folders, if you'd like to avoid the objects getting affected/changed.
Before giving any answer, we first need to know how exactly those "deployment packages" are constructed. Does a "deployment package" equal a deployment group? One XML file? Something else?
@swa, please explain how exactly you perform deployments in your landscape and whether you work with versioned repositories or not, then only can we give educated answers.
And please also tell us what PowerCenter version you use on what HW/OS platform.