Yes, they’ll be fine.
The Digitakt uses a “fingerprint” (technically a hash code) of the sample as the reference from projects and sounds that use it. Renaming the sample or moving it to a different directory doesn’t change the fingerprint, and so the projects and sounds still reference the correct sample.
It works even if you delete a sample entirely, and then re-transfer exactly the same samples again! Amusingly, if you transfer the exact same sample file twice, so you have it in the Digitakt under two names, - and load one into a project slot, you’ll see the other listed as loaded in that slot, too!
(Warning: The delete and re-transfer thing may not work if you let Transfer sample rate convert, since then the samples may not be exactly the same second time around…)