TYPO3 Core

I've got a weird problem. When I add a composer.json to a already installed extension e.g.

{
"name": "test/myextension",
"type": "typo3-cms-extension",
}

and reload e.g. the EM the following lines are will be added to the PackeStages.php file:

[...]
'manifestPath' => '',
'composerName' => 'test/myextension',
[...]

IMHO this is fine. In some circumstances it seems not to work. When I deploy the EXT (the only thing which has been changed is the composer.json) to several systems, these necessary lines wont be added to PackageStages.php SOMETIMES! When this lines aren't present it will break the dependency tree and the EM is not accessible anymore. Unfortunately I cannot reproduce this issue so I'm a little bit lost. When I test is manually it works, but in some cases these lines are definitely not present.

Is it possible to force the regeneration of PackageStages.php?