It sure can be problematic if one doesn't keep the filing system they choose in order and without deviation... I personally use separate external hard drives to store the E-PUB's .pdf's and any other digital format so that they don't get mixed up with what I usually have in either one of my desktops or my laptops as well...
Any music or movies are stored separated also in a different hard drive that can hold greater capacity (4Tb) with each file anywhere format least 1 Gb to the largest one so far being 44Gb... Yes indeed! One must be very vigilant in assuring that their filing system is in order and working as efficient as can be... It's definitely something not to become complacent with as I have experienced when I first started organizing my digital content... Those days were very confusing and complicated as opposed to the K.I.S.S method I use currently...
Having said that, I still keep my printed books at the ready for quick and easy access when I'm @ home... So much to learn and so little time left to take it all in.
Respectfully,
Henry