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I can't replicate this here but I can see how it might have happened.

If you never went to the Settings tab and clicked Save there, then the tag for keep_settings wouldn't be present in the configuration.

When this package was updated for PHP 8.x, it changed like so:

-       if (isset($config['installedpackages']['freeradiussettings']['config'][0]['keep_settings']) &&
-           empty($config['installedpackages']['freeradiussettings']['config'][0]['keep_settings'])) {
+       if (!config_path_enabled('installedpackages/freeradiussettings/config/0/', 'keep_settings')) {

Those two tests aren't equivalent. The first tests that the tag is there at all, the second tests if it's empty or not. The new test only checks if the tag is present, which isn't sufficient.

For the old test to be true it had to be present in the config but empty, which means someone saved the settings with that option unchecked. Now it's happening both when that is true and when it's unset, which is also the case if someone had never saved the main settings tab, which shouldn't be needed if the default settings are OK.

I confirm that the <keep_settings> tag is not present in my config.xml.
After entering settings and saving, the <keep_settings> tag appeared on config.xml: value "on" when "Save settings after deletion" is checked, value "" when it is unchecked.

By reinstalling the freeradius package with <keep_settings>on</keep_settings> the configuration was not lost.

Paolo Rosso wrote in #note-7:

I confirm that the <keep_settings> tag is not present in my config.xml.
After entering settings and saving, the <keep_settings> tag appeared on config.xml: value "on" when "Save settings after deletion" is checked, value "" when it is unchecked.

By reinstalling the freeradius package with <keep_settings>on</keep_settings> the configuration was not lost.

The package available on Plus 23.05.1, CE 2.7.0 was fixed yesterday and if you reinstalled after my last update yesterday then it would have worked properly no matter how you had it set. So if you want to try it again without the main settings present, it should have the proper behavior now.

Tested on
23.05.1-RELEASE (amd64)
built on Wed Jun 28 03:57:27 UTC 2023
FreeBSD 14.0-CURRENT

freeradius3 0.15.10_1

After uninstalling/reinstalling freeradius, I can confirm that the settings are not deleted and are retained.