WooCommerce holds 300 characters, eBay takes 50
Six times the room on one side, and the shorter limit is the one that governs.
Items pair up by SKU, so the shorter of the two limits decides what your naming scheme can be. WooCommerce will store a SKU up to 300 characters, which is more room than any catalogue needs. eBay takes 50. Anything longer is truncated on the way to eBay, and a truncated SKU no longer matches the item it came from, so the count for that item stops moving.
Nothing errors when this happens, which is why it catches people out. We send the shortened SKU rather than refusing the item, so no listing turns red and no warning appears anywhere. The item simply stops pairing with itself, and you find out weeks later when the eBay count and the WooCommerce count disagree by a few units and nobody can say when they parted.
Fifty characters is enough for a sensible code and not enough for a sentence. If your WooCommerce SKUs were generated from product titles, that is where the trouble will be, because nobody ever had a reason to shorten them. Export your catalogue, order it by SKU length, and deal with the top of the list in one pass before you connect anything.