It means that you had a deep understanding for a few seconds, and then lost it. Or that you got trapped in the same confusion as the author, absorbed what made it seem appealing, and then "corrected away" the confusion.

To determine which one happened, try the following:

• reading it again
• rephrasing it in your own words as many different ways as you can
• seeing how the thesis connects to other topics, and if that connection can be independently verified

Eventually, you should be able to either gain the understanding, or recognize where the error is.