Hi Marcin Bodziony,
Thank you so much for your further reply and cooperation.
Judging from your capture, when the cursor turns into circle, it means Visio app is trying to process your modification and save your changes. The vanishing situation you’ve encountered I’m afraid may be a background error that Visio failed to save your changes which is apparently abnormal. Again, I apologize for the inconvenience situation you’ve encountered, and I do deeply understand it.
In that case, as I mentioned in my last reply, I sincerely suggest you can contact your IT department to help your tenant to update your Visio to the latest and check whether the issue persists or not.
If the issue persists after updating to the latest version, since you mention this issue didn't happen before and this situation happens globally in a tenant level which affects to all users in your environment. I’m afraid this issue needs to be reported and investigated from back end to find the cause. The Microsoft Support Team has higher permission to remotely assist you and collect background logs for the root cause. This is a more efficient way in handling this case for you.
If you are an admin, I recommend you get support by following steps from this link: Get support - Microsoft 365 admin | Microsoft Learn to raise a support ticket from admin center or calling the phone support to contact Microsoft Support: Customer service phone numbers - Microsoft Support.
If you are not an admin, you can contact your admin to contact Microsoft support. You can look for the way to find your admin through this link: How do I find my Microsoft 365 admin? - Microsoft Support. (usually, your IT department have the admin privilege)
Please accept my apologies for redirecting you to the related team support, as the moderators in this community have limited resources and permission to verify the backend information and to get the quick and better assistance, we requested for this.
Greatly Appreciate again for your patience and understanding, and sorry again for this inconvenience you've encountered.
Hope you also having a great day today and wish you a brilliant year ahead as well!
Sincerely,
Harry | Microsoft Community Moderator