how should I label components changing between PCB versions?
Leave the holes, it lets the schematics and the PCB indicate a mismatch if someone has to repair or diagnose such a device one day in the future.

Many consumer circuit producers number their resistors starting at round numbers to indicate the general circuit area involved.  So radio parts starting in 100 may be the RF circuit, those in 200 may be the pre-amps, and the ones at 500 may be the audio amp components.  Changing a part in one section will not affect the others even if you were to add another resistor it may increment the component number only in the local group and everything else is as before.  It lets you reuse circuit sub sections easier.  These days renumbering is much easier but some of the old reasons still have utility. Basically premeditated holes in the numbering system.

EDIT:
It also lets your Bill of Materials (BOM) maintain internal consistency over the versions.  It will also generate more human readable file comparison diffs if resistor R203 is removed and R209 is added instead of resistor R203 removed and R203 added with a different value or watt rating (or what if the value and power stay the same the BOM diff will show no change after the circuit version was revised).  If you have made a change to the value only then the diff will be descriptive too as it will indicate the change and you will know that no parts were removed or replaced, just the value or the particular circuit component R203 was changed in value.

Also if you have to provide replacement components to a service agent in future you will have to have each part number classified by revision as they may be different.  If you were to add or remove just one component and renumbered ALL the parts following your admin will become very expensive.

Once the circuit is published (leaves your office/factory) it would be prudent to lock as much of the documentation down from spurious changes.  If it is the Mark 2 with vector field nullifiers and no longer the proton precession coils you could have a totally new product and keep the documentation separate.