Clipping mask disappears after reopening Illustrator file, leaving transparent shape instead

Thank you.

I can reproduce the issue. Probably the culprit is that you are creating the clipping mask with a nested group serving as the clipping path(s). Obviously some kind of invalid construction.

If you simplify that and just take one plain path to clip, it should work as expected.

Below is a sample file. On Artboard 1 there is the unwanted behaviour. On Artboard 2 there is the expected behaviour.

Check the Layers panel to compare.

North Africa