Make sure to execute the steps in the proper order. It is your responsibility and Alfresco does not offer much support here. For the sake of an example, let's assume you are removing a mandatory property. I would do something like this:
- Upgrade the model and make the property optional
- Remove the value from all content instances
- Upgrade the model with the property removed
This example should work without an index rebuild. Other changes, such as when you change how a property is indexed require an index update. If in doubt, rebuild the index.