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Magento broken after module disable

I have a huge problem with Magento on a live platform. I've disabled a few modules, which I don't use, via a command line. I've made it before already and had no problems with it. But now I can't upgrade or deploy. I get this error:

Invalid argument supplied for foreach() in /vendor/magento/module-store/Model/Config/Processor/Fallback.php on line 125

I've enabled the modules again, but the error stays.

What could I do? Appreciate any help.