Hi Juraj,
Thank you for reaching out. If there are resolved comments on the published prototype you can see them using the filter at the bottom right of the comments panel as shown in the screenshot below.

Here are some more details about the topic -https://helpx.adobe.com/xd/help/review-and-comment-design-specs.html.
In order to avoid this situation, you can create a new link for your clients. However, deleted comments shouldn't be there.
Can you confirm that you see deleted comments on the published prototype and not the resolved one? It would be great if you could create a new prototype and test it out, and even better if you could share the prototype with me so that we can investigate.
Awaiting your response.
Thanks,
Atul_Saini