For sure, it might. But shouldn’t happen ever since trash contains deleted pieces that shouldn’t be audited unless a satellite recovery took place just after removal of trash. And if you’re such with your filesystem because it’s full, it might be an ultimate measurement in my opinion, posing only a very low risk on DQ.
Essentially, the TS wants a inplace conversion from exFAT to ext4 or something. Since the disk is nearly full, I don’t see any visit options to do so. By if you see one using gparted (which -as fast as my knowledge stretches- means data loss by default, if you haven’t shrunken the underlying file system; which is not possible with exFAT and a full drive) or LVM, enlighten us!
My advice would be to carry on for a while, till you’re around to fix it at location. Or just accept the situation of being unable to use the full size, may be partially due to the cluster size (at least 4KiB by default) of exFAT as Alexey already suggested. Which means an average loss of 1-2KiB per file. Although, taking one node here if currently about 400GB in 2000000 files, it would waste not much more than 40GiB (calculation:
2E6 / 400E6 * 4E9 * 2048/10243). So there must be another explanation.
Dit you already run fsck.exfat / exfatfsck from the exfat-utils package?