The important thing is to be recovered for key workouts. It sounds like you weren’t, so you made the right decision. (I probably would have also skipped the pick-ups though.)
If recovery between key sessions is taking longer than planned and interfering with your progression, then reduce the load. That could mean making the long runs shorter and/or the high-intensity sessions lower volume (shorter or fewer intervals).
As you train year after year, you’ll be able to tolerate more, and your recovery will improve.