Hi Mike!
I have emailed you. Please check your inbox for design files. Thanks!
I was able to experience the clipping paths being lost after reopening the file.
There were some additional paths, of the circle shape and by deleting them, then clipping paths began to hold.
First I made you artwork into 3 layers it simplify so I could concentrate on the problem area. I moved a few circles over so you could se the extra paths that I deleted


So basically there were few extra circles in the mask.
A technique I use to make mask is I assign the mask a total different (dummy) color than the contents. That helps confirm my mask is on top. I select item and hide them and the mask, then I unhide so only the elements I wish to mask are selected.

After you make the mask that dummy color disappears.
