It can cause issues if you change it, so it's not supported to change it in a project unfortunately.
See: Create Projects, Teams, and Tasks - CA PPM - 15.4.1 - CA Technologies Documentation for more details.
However, I know at times customers may accidentally set the wrong % Complete Calculation method and have to change it (Example the % Complete Calculation Method that is supported with MSP is Manual so if a customer is using a different method it causes issues). In those types of circumstances, I'd recommend testing it out in non production to measure the impact to the data in projects to make sure it doesn't cause any negative side effects and be aware it would be at your own risk if you do hit a data issue. An example of an issue I found reported is when a project was set to manual to update the % Complete for tasks without assignments. When the customer switched the % Complete calculation to Effort, the customer then lost lose those updates to those tasks.