Just clicked on the "see all" button to view lists studying on. Due to studying lots of small lists through ChinesePod not all my lists are visible.

"See all" only shows 50 lists. I'm worried that earlier lists studied are not being studied...

They are. I think what you see sort of is my fault. I have 1000+ Chinesepod lists and as a result I could not even load the study page. To help me me out the team did put some limit on how many lists where shown/loaded. You still study them all etc though. Note, on the Beta site all your lists will be shown.

I think this could be improved. There are some lists which I am half way through studying and paused, but want to pick them up again it would be easy if I can access them in the study section.

One possible way, which I requested a while back (because the amount of lists was too great) is to groups lists together, e.g there could be some sort of drop down to view the CPod lists, custom lists, etc

or a way to merge two related lists into one custom list, possibly?

We set up the 50 list cutoff as a stopgap measure until we implemented a real solution. That real solution is done and on beta, so switch to beta to try it out. The fix will be on live later this month.