Hello Danielle,
I don't see how this is possible, since it's something I have had to specifically address more than five years ago.
Joomla will prevent the package type extension to be installed if any of the included extensions failed to install. The only way to prevent the accidental downgrade of FOF or FEF is to fail their installation. This would of course mean that if these two extensions are listed in the XML manifest of the package type extension you can never install it if you already a newer FOF or FEF version already installed.
My solution to that was to not list these two extensions at all in the package extension's XML manifest. If you extract the ZIP file and open the XML file you will see they are not listed. So how are they installed?
We actually do that in the preflight() method of the package script. We ask Joomla to install these two file type extensions. If they fail to install they do output warning messages (these come from the Joomla! extensions installer internals and cannot be suppressed) but we also add another message of our own which pretty much says "please ignore the ‘Custom install routine failure’ message". Since the installation of these extensions is not part of the package manifest itself the package extension will install just fine.
So what really happened is that did get a message that you can't downgrade FOF and / or FEF BUT the actual extension (components and plugins) DID get upgraded regardless. If this didn't happen you have a different issue and you need to check the warning messages you got after the FEF / FOF no-downgrade messages.
Nicholas K. Dionysopoulos
Lead Developer and Director
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