Hi Svetlana,
Thank you for your interest in Syncfusion products.
I am afraid that I was unable to reproduce the mentioned issue in FlowLayout while changing control visibility. I have tested the issue with simple sample and attached a sample file in following link
http://www.syncfusion.com/uploads/redirect.aspx?&team=support&file=Form11455772168.zipAlso please refer the documentation from below link to rearrange the control in FlowLayout.
http://help.syncfusion.com/ug_82/WindowsFormsUI_Tools/RearrangingTheControlsLaidOutByFlowLayoutManager.htmlPlease have look at the above sample and let me know if you still face the issue. Could you please try to reproduce the issue in above sample that would be helpful for us to provide a better solution?
Regards,
Lingaraj S.