I don't see why the removal would be an issue and the replacement with links, assuming they're identical to the versions that were included with the Matlab installation. But somehow this feels like you're making a lot of work for yourself.

When I used to support a group where we maintained many versions of proprietary packages such as Matlab, our group would install them into self contained directories and use a tool similar to modules to maintain the management of the user's environment when they would want to switch it so they could use these packages.

See this U&L Q&A titled: Add multiple subdirectories under the same parent directory to PATH where I discuss various tactics for managing a system's $PATH environment variable. These same tactics can also be applied to pretty much any environment variable. These are often what controls the functionality of proprietary applications.

I don't see why the removal would be an issue and the replacement with links, assuming they're identical to the versions that were included with the Matlab installation. But somehow this feels like you're making a lot of work for yourself.

When I used to support a group where we maintained many versions of proprietary packages such as Matlab, our group would install them into self contained directories and use a tool similar to modules to maintain the management of the user's environment when they would want to switch it so they could use these packages.

See this U&L Q&A titled: Add multiple subdirectories under the same parent directory to PATH where I discuss various tactics for managing a system's $PATH environment variable. These same tactics can also be applied to pretty much any environment variable. These are often what controls the functionality of proprietary applications.