Hello Stacey,
this is a quite common issue with Yahoo lately and upon inspecting the problem with numerous users, all we found is that it’s unfortunately a server side issue that we cannot do anything about.
Please contact Yahoo support about their server changes.
This same issue is very common with @hotmail.com email addresses. I have one, and very often the server is having problems or Microsoft is working on their Hotmail site. eM Client eventually gets all email when their server is up and running.
One solution to this problem, of course, would be to move to a different email provider, such as Google’s @gmail.com. They rarely have problems from my experience but the move might be a bit inconvenient to do. Perhaps setup a Google account AND keep the Yahoo account, too? Then you could slowly make the transition, or just keep both. I have 4 email accounts but only really use two of them - @comcast.net and @gmail.com.