The way that "link parameters" work is by providing the parameter on the URL of the portlet-page that we link to. Therefore, if your NSQL code in "Portlet2" always picks up that parameter from the page URL then that parameter is never "cleared".
So there is no simple answer to your question.... you could;
1) have another copy of the portlet on a different portlet-page - get the user to use that when they want to use alternative parameters
2) train the user to edit the URL, removing the link parameter from it
3) code your NSQL in'portlet 2' to ignore the URL parameter if any normal filters have been used (this would require that all your normal filters in 'portlet 2' would be coded as WHERE:PARAM filters rather than automatic ones).
Option 1 is the easiest (and what I would do), option 3 could be "seamless" from a user point of view, but its a rather over-complicated solution I feel.