Will 256GB of RAM work on my X99 motherboard with an E5-2699 v3?

Yes, it will almost certainly work if your motherboard has eight DIMM slots and supports 32GB RDIMMs. The E5-2699 v3’s memory controller handles registered DDR4 ECC fine, and ECC will enable automatically. However, check your board’s manual for BIOS support of 32GB modules and rank limitations — populating all eight slots with dual-rank sticks may push the memory controller’s limit. Buy known-good RDIMMs from a reputable seller.