Missing links - (aka link loss) occurs often when upgrading a website from one CMS to another or from a static HTML site to a dynamic php powered creation. Whenever you change a URL for a page you risk losing the ability for existing links pointing to the page to find the new URL. A simple example is when you change 'contact.html' to 'contact'. You change the links on your own site to point to the new name of that page but how do you deal with the links on 45 other web sites that are still pointing to 'contact.html'? And the all important question, why should you care? First, you should care a great deal because when people click through on those 45 sites they land on a '404 not found' which usually causes people to give up on the content they're trying to find and surf another wave, often to a competitor's version of that content. Losing relevant established traffic hurts your purpose in having a web presence in the first place and will slow your growth.
Back to how to deal with the problem, unless you have control over those 45 sites or you want to take the time to contact all those site owners and tell them to update their doggone outdated links, your options are few and require somewhat advanced code knowledge, particularly dealing with the htaccess file. Any time you mess with files in your FTP or cpanel folders you had better know what you're doing or your site may melt into whiteness (wsod - white screen of death*). In your htaccess file you can add redirect instructions so when people click a broken link pointing to your site you can redirect them ... Any which where you want. I recommend you usher them directly to the new location of the content you updated. Depending on how many updated pages you have, you may be adding a lot of redirect rules. Or just one to take them to your site search page and let them find their own way. You at least want to avoid a bunch of unnecessary 404's and flustered web clickers. Here's an example of a few lines of code to accomplish this:
Make sure you have enabled the Rewrite engine and that your server is configured for this type of action.
*The wsod provides no clues as to why your site is broken so you have to look at your error logs in cpanel or via root access and then correct the problem. Sometimes it's due to insufficient memory during a process or as the vacuum people say, a loss of suction.