Yes, the same sample can be used in multiple barcoding runs (Day 1s).
At the end of fixation, cells can be split into several aliquots for future input into barcoding plates. Simply calculate the number of cells needed to input into the Day 1 plate, and aliquot the corresponding volume of fixed cells into as many 1.5ml tubes as desired. Store at -80C until needed (up to 6 months).