I can confirm the behaviour I reported in the OP. I repeated the steps as given below and "lost" the MoodleBox plugin!
- R Pi 3 A+
- Make a MoodleBox 4.5.1 (It has Moodle 4.1+)
- Git upgrade it to 4.1.14. Kick the upgrade from the web interface. Slow, but finishes.
- The plug-in page detects that the MoodleBox plug-in needs an upgrade
- Do the upgrade (on the 'admin' GUI). All goes successfully.
The new directory ./admin/tool/moodlebox is there (and readable to the web server). The version.php has:
$plugin->version = 2024032801;
$plugin->release = '2.17.5';
$plugin->requires = 2018120300;
$plugin->supported = [36, 403];
$plugin->maturity = MATURITY_STABLE;
$plugin->component = 'tool_moodlebox';
But the two MoodleBox links are gone from the bottom of the Site administration > Server page!