The Download ID seems to be removed from the extra_query when you update an extension. I've seen that happening with JCE Pro as well so it doesn't look it's an issue we caused in any way. More frustratingly, I have not seen it happening in all sites. My sites (development, testing and live) seem to have survived. My wife's sites were affected. We are both on the same host. I have no idea why this happens on some sites but not all of them. It seems that the sites which failed the installation of the first Akeeba Backup 8 and Admin Tools 6 versions were the ones also affected by the Download ID disappearing from the extra_query in #__update_sites. Correlation doesn't mean causation because on my test site where I inflicted the same problem with updates I can't seem to be able to reproduce the extra_query being cleared.
As for why the Download ID cannot be applied, I can tell you why since I've debugged this issue this morning on an affected site that belongs to my wife (it really helps that we are working from home on adjacent desks). Joomla 3.9.25 introduced yet another bug, this time with the XML forms' hidden field. This is used in the Admin Tools config.xml file which is rendered by Joomla's com_config when you click the Options page. The bug is fatal on PHP 8 but merely a warning on PHP 7. However, on PHP 7 it causes clicking on Save & Close in the Options page (which is rendered by Joomla itself) to redirect you to the public homepage of your site instead of taking you back to Admin Tools. This makes managing your Download ID in Admin Tools very hard. Since the Options are rendered by com_config we have no way of adding a post-save hook. What we do is ask Joomla to pretty please redirect back to Admin Tools' Control Panel page which detects the change in the saved Download ID and applies it to the #__update_sites table. Since this redirection is broken the code doesn't run which is why you have this problem. This is a Joomla 3.9.25 problem, not an Admin Tools 6.0.4 problem.
You will need to follow a workaround.
Go to Admin Tools. Click on Options, Update. Remove your Download ID. Click on Save. Go to Components, Admin Tools. This clears the extra_query and tells Admin Tools a Download ID is needed. In fact, it should prompt you for a Download ID at the top of its Control Panel page.
You can either use the prompt to enter your Download ID or follow the manual approach: click on Options, Update; enter your Download ID; click on Save; go to Components, Admin Tools. In both cases the #__extensions table is updated with the new Download ID, you are back to Admin Tools' Control Panel page and the extra_query is updated in the #__update_sites table.
However, this is not enough if an update (e.g. 6.0.3 to 6.0.4) has already been found. Instead, you need to follow the next steps in precisely the following order to work around another bug in Joomla.
Go to Extensions, Manage, Update. Click on Clear Cache.
Now go to System, Clear Cache which is a completely different page that has a confusingly similar name. Click the drop-down menu on that page that currently reads Site and choose Administrator. The page reloads. After the page reloads click on Delete All in the toolbar.
Now go to Extensions, Manage, Update. Click on Clear Cache.
After the page reloads click on Clear Cache again. Seriously, this is required. I know it makes no sense, but you really do need it because the first Clear Cache may not update the last update check time in #__update_sites according to my debugging.
Now you can click on Find Updates. After the update to Admin Tools is found you can install it just fine.
In case you lost track, this is three (3) different Joomla core bugs you need to work around. I have been reporting two of them privately since 2014. No action taken from the project. I made a public report on March 5th and was met with open hostility and threats to our company. So, no, I won't bother reporting the third one. They just don't care or at least they treat me like garbage ever since my first ever bug report to the Joomla project all the way back in 2009.
I would very much prefer if we didn't have to use the completely broken Joomla extensions update feature which causes all these issues. However, the Joomla project FORCES us to use it since 2017 on pain of permanent removal from the Joomla Extensions Directory.
Nicholas K. Dionysopoulos
Lead Developer and Director
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