Introduced in the middle of February, Pokémon HOME allows for transferring from Bank and Let's Go Pikachu / Eevee as a central storage site with connectivity to Sword & Shield.
When a Pokémon is transferred from Bank or Let's Go Pikachu / Eevee into HOME, it is assigned a unique 64 bit number to differentiate it from other uploads.
Pokémon that have not yet visited HOME do not yet have a HOME tracker.
Pokémon that are traded in-game without HOME do not get assigned a tracker (SW/SH <-> SW/SH).
Pokémon that must travel thru HOME to reach the game it resides on must have a HOME tracker (SW/SH origin do not have a tracker).
Pokémon that are uploaded in the same batch are not guaranteed to have a similar tracker (usually incremental).
Pokémon that aren't yet in the PK8 format cannot have a tracker value assigned (Bank did not track). It is only a concern in PK8 format.
What exactly might this value be used for?
Differentiation of unique uploads, to prevent users from depositing & withdrawing the same data to boost their counts.
Tracking how Pokémon are traded between users.
Detecting if a Pokémon has been modified from the original upload.
Detecting if a Pokémon is foreign from the HOME system (having a value of zero).
When Pokémon with the same Tracker value are uploaded to HOME, they are discarded (deleted). It only retains the first unique Pokémon with that tracker value, on a per-account basis.
It appears the best practice is to let the server assign you a tracker, rather than having a blatantly wrong tracker. Historically, GameFreak does not obsess over this metadata, so having arbitrary/lacking tracker values might not matter at all.
Only HOME can determine if a tracker value is valid.
Due to the described behavior, here are our recommendations:
When cloning Pokémon in Sword & Shield, clear the tracker value for all clones you create.
When creating new Pokémon that are from prior generations for Sword & Shield, leave the tracker blank and transfer it to HOME.
When creating new Pokémon that originate in Sword & Shield, leave the tracker blank.
When modifying Pokémon that have already visited HOME, zero out the tracker if you change anything that can't be changed in-game.
Why not create a random tracker value?
Again, only HOME can determine if a tracker value is valid.
HOME can possibly check tracker values to see if the details match the original upload (modified data).
HOME can possibly check tracker values to see if the details are on another user's account (cloned data).
Uploading to HOME without a tracker value will automatically assign a new one.
You can receive Pokémon that lack a tracker value from other players via trade (in addition to SWSH natives).
PKHeX's default settings are to ignore missing tracker values (should be on every non-Gen8 origin Pokémon that is residing in Gen8+), but has a toggle setting to opt-in for strict checking. This is to allow users to create the most-legal data without forging an INVALID tracker value, which will be legal after transferring in & out of HOME.