First, which site are we talking about? I'm assuming
http://jacksretail.com, right?
Second, how are you determing which pages have been dropped? and what are those pages? I assume you do not have 50,000 separate pages on your website so I'm guessing you mean pages linking to your site, aka "backlinks"?
For backlinks, entering +"jacksretail.com" into Google just now I see "about 42,700" entries found. However, if someone else does that or I return in hald an hour and try again, I'll probably get a somewhat different result - or at least that has been my experience in the recent past.
Google has always emphasized that they only provide "a sample" of backlinks and rumor has it (emphasis on the word rumor there - I don't think anyone has really confirmed this) that Google is making those results even more variable than previously to discourage excessive checking by site owners and
SEO operators.
Add into that the changes Google has been making in recent months that may have meant that some very low or questionable pages linking to you in the past have dropped out of sight in the database or been penalized and dropped altogether, and what this means is that in truth you may not have lost anything that was beneficial to your site at all.
Of course, I had to make two assumptions about the question you were asking so I may have been addressing either the wrong site or the wrong question about that site...