To reproduce:

• Drop a sword close by
• execute

/data merge entity @e[distance=..3,limit=1,type=item] {Item:{Enchantments:[{lvl:1,id:"minecraft:sharpness"}]}}

• ->chat says "modified data of sword"
• nbt stays unchanged

i've already tried f.ex. making an armorstand invisible, that worked though.

also giving yourself a sword with the same nbt (without Item:{} obviously) works as well