I have done significant research into this. There is no way to do this (though it's such a common use case where someone already has an active fan page and launching an app later)
Earlier every app used to have a profile page (which was not like fan page) and facebook at the start of the year gave ever app admin to move their likes to another fan page. This option has been removed.
There is another way that I have discovered.
- Create fan page for the app (from app details section) by clicking "Create Fan Page"
- Goto pages and select this newly created fan page and rename it to be the same as the other active fan page(with which you initially wanted to link to). This is needed because merge option appear when 2 pages have same name and same category.
- Goto your active (original) fan page, click edit page, goto resource and click on merge pages and do the marge.
However as someone has already reported, there is a bug in the system, on merging it removes the app link (something that will be fixed soon). Here is the link to the bug.
http://developers.facebook.com/bugs/413029272079414?browse=search_5033475a2a50c9f73780526