What happens after I delete a preferences file from Matlab? Will the Matlab preferences be restored the next time I open the program?
If so, where does Matlab build this "built-in" preferences file from?
Not somewhere user-accessible, if you're hoping to be able to modify how that preferences file is recreated.
Would it be recommendable to check for preferences within the startup.m file?
Why? What preferences are you interested in, and what do you want to decide or do based on the preference value?
What should be the best practice for this?
I would caution against trying to manipulate the preferences file. The format of the entries in the file is not documented. Many of those preferences are likely available via the Preferences icon in the Environment section of the Home tab of the Toolstrip. If there are preferences you want to be able to set that are not accessible from the Preferences UI, you can submit an enhancement request to Technical Support using the telephone icon in the upper-right corner of this page asking for them to be added to the UI.