Moving a site collection to a new content source

Here are the steps to move a site collection (from within a web application) to a different content source. This process has its own pros and cons and you should analyze the impact before deciding to do this step.

Scenario:
You have one content source (Local Office SharePoint Server sites) with two web application configured inside it (http://webapplication1.com, http://webapplication2.com). You need to move one site collection from this webapplication1 to a different content source so that you can crawl this site collection more frequently and quickly rather than crawling the whole web application.

Attempt 1
Created a new content source - SiteCollection1
Tried to enter the site collection url (http://webapplication1.com/sitecollection1) and it gave the following error: "The start address http://webapplication1.com/sitecollection1 already exists in this or another content source"

SharePoint will not allow you to enter a site collection in the content source if the parent web application is already specified in the same or in another content source.

Attempt 2
Removed the web application entry (webapplication1) from the main content source. Mentioned all the site collections separately in the main content source. Mentioned the single site collection in a separate content source.

Advantages: The site collection can be crawled separately whenever needed. This is much faster rather than crawling the whole web application.

Disadvantages: When you remove the web application entry from the main content source, all the index related to the web application are deleted by the gather and they appear as a warning in the crawl log. You will have to do a full crawl of the main content source again (where you have all the site collections mentioned) to get the content indexed.