You could do that, if your only concern was to make sure the chip count was correct. But a better way to do it is to adjust a player's chips received when they buy-in. Unless you're using Simple Mode, you can adjust any of the values that make up a transaction. Meaning, if for example players receive 5000 in chips for buying in, you can adjust this amount for any individual buy-in when you buy players in. So when you buy-in players who are "on time", you could adjust the chips they receive, say for example add 500 for a total of 5500. You do this in the Buy-in window (not on the Game tab of the Settings window). Once everyone who was on-time have bought-in, you continue to conduct buy-ins but you just don't adjust the Chips value.
An even better solution is to create buy-in profiles. It makes it a little easier to deal with, and is more efficient and less error-prone, especially when you may change multiple values. Say for example you not only awarded additional chips for players who arrive on-time but you also gave them points. By using profiles, you simply select the correct profile for the player buying in and the software will set the correct values.
My favorite example is similar. Let's say you give extra chips to players who arrive early, and you also penalize players who arrive late by giving them fewer chips. You can create 3 profiles: "Early arrivers", "On-time players", and "Late arrivers". Then when buying players in, you just select which of the categories they fit into.
To do this, press the "+" button next to Buy-in on the Game tab:
Give the profile a name, like "Early arrivers". You'll see a new profile added to the list of profiles (if you haven't done this before you probably didn't even know it was a list):
Fill out the values for "Early arrivers" appropriately. The new profile's values will be copied from the master profile, so if you set the values for the master profile for your "on time" players first you'll only have to change the "Chips received" in the "Early arrivers". Otherwise, make sure you set all the values appropriately.
Repeat this for "Late arrivers". Now you have all 3 profiles. If you want, you can rename "Master" to something else, like "On-time players". To do that, press the "Gear" button, select the "Master" profile and press the Rename button:
Now when you buy-in players, just select the appropriate profile and all values will update:
