Regenerating the system in SOPC

The answer depends slightly on which version of the tools you are using.

Prior to 7.1 : After making changes to your HDL code, Right click on your custom component in the IP catalog on the left side of SoPC Builder and click Edit Component. It will bring up the component wizard and automatically re-analyze your HDL files. After saving the component, you SHOULD delete any instances of the component in your system and re-add them. I say should because if the actual avalon interface didn't change at all, you don't really have to remove and re-add the component.

7.1 and later: If the changes you made to the HDL do not affect the avalon interface or component settings at all, then do nothing. Components in 7.1 and later are compiled in as user libraries under Quartus. You can change the HDL code at will. If the changes you made do affect the avalon interface or component settings, then you should Edit the component to make any necessary changes. However, you do NOT need to remove and re-add any instances of your component. SoPC Bulder 7.1 and later will automatically detect those changes normally.

Jake