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however if you remove one of the ISR's, then turning the encoder will cause a reset of the Arduino and we go back to the top of the loop.
This is because you have enabled an interrupt without a corresponding interrupt service routine(ISR).
I plan to use the encoder to increment and deincrement a variable, but if I need two ISR's I am not sure how it will impact the rest of the code?
I do not use that library, so I'm not familiar with the details, and whether or not there is the option to use one interrupt. Using one interrupt instead of two will cut the resolution in half. For menus, this can be used to align the detents with the counts.