Could anyone please share the views if we want only 1 link from the home page of a sub domain and disavow rest of all hundreds of backlinks from that sub domain?
Google looks at many things statistically. It's a dumb machine with a superb ability to correlate, an excellent sense of the odds, and a very long memory... so it's not as dumb as you may be assuming, and it's gradually getting smarter.
Those "hundreds of backlinks", along with other signals from your site, have already provided Google with a strong indication that the original links were not natural (ie, that they were not freely given editorial links). "Hundreds of links" suggests a special relationship between the linking site and your site, which makes Google think that there might have been some manipulation going on.
I would not assume that Google won't notice if you don't disavow that juicy link from the home page. It was undoubtedly part of the original deal, and Google's not likely to forget it. And the home page link is the link that Google knows that someone manipulating links would want to hold onto. Because of that history, it's now tainted. Google's aware of the odds that there was a relationship, and it knows your history... so you can save yourself a lot of time and grief and treat these things on the domain or subdomain level and disavow the entire package.
This is what Matt Cutts was talking about regarding using a "machete", when he answered a question about problems he was seeing with disavow in his blog post... What to expect in SEO in the coming months May, 2013
One common issue we see with disavow requests is people going through with a fine-toothed comb when they really need to do something more like a machete on the bad backlinks. For example, often it would help to use the "domain:" operator to disavow all bad backlinks from an entire domain rather than trying to use a scalpel to pick out the individual bad links. Thatís one reason why we sometimes see it take a while to clean up those old, not-very-good links.
Barry Schwartz followed up with some further details at Search Engine Roundtable... Google: Use The Disavow Tool Like A Machete & Not Fine-Toothed Comb
And we had some follow-up discussion in this thread here... Matt Cutts on stages of Penguin recovery June, 2013
In general, I would not try to hold on to favorite links from domains that are no longer trusted, and I wouldn't try to add variations to previously arranged inbound anchor text in an attempt to rewrite history.