When you summon a lighting over the water on yourself, you can see that the lighting texture become invisible and it's "deletes" the water (shows texture under the water block(s) as if there was no water instead of lighting strike/white texture.
How to reproduce:
1) Go over the lake or piece of water (around 1 - 3 blocks deep)
2) Use /summon lightning_bolt
3) You will see water texture & white lighting bold texture disappear for a split second and instead of those you will see ground below water
Thank you for your report!
However, we are already tracking this issue, and this report is a Duplicate of MC-188203, which has been marked as Won't Fix - while this behaviour is not desirable, the developers have said that they will not or cannot fix it.
Please use the search function in the future to prevent duplicate reports.
Quick Links:
📓 Issue Guidelines – 🛠 Community Support – 📧 Customer Support – ✍️ Feedback and Suggestions – 📖 Game Wiki
💬 Mojira Subreddit – 💬 Mojira Discord