I cannot reproduce your issue. To be clear, I installed Admin Tools 5.3.4 on a Joomla 3.9.11 site and upgraded it to the same dev release I told you to download. No problem.
Moreover, I created a new Joomla 3.9.11 site where I installed Admin Tools 5.3.4. I deleted the admintools_scans table as I told you to do and installed the Admin Tools dev release. Again, no problem.
Also, to be sure that I've covered all bases I created yet another new Joomla 3.9.11 site where I installed the dev release of Admin Tools (fresh install, not an upgrade). No problem either.
Furthermore, the SQL query that you have a problem with is not something that happens during installation of our software. Are you getting this problem when you do something else, after you have installed our software? If so, exactly what? I don't even know which "button to fix the table" you are referring to.
I think that you are describing your interpretation of what is going on, not what is actually going on. Please be very specific about what you do. Use screenshots if you cannot put it into words.
Nicholas K. Dionysopoulos
Lead Developer and Director
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