@ioannis.compet 

Are the clients that are not visible part of the IOT devices?
Are static IPs set for these devices?
What is your network topology?
Does it all show up in the Client list before the upgrade?

@ioannis.compet 

 Actually I think also need you to provide a complete topology diagram of your entire network and need to know how these devices are connected?
This will make it easier to pinpoint the problem.
Are these devices not shown in the controller's list of wired and wireless devices?
Or are there any advanced settings set on the controller?

@ioannis.compet 

So what is the model number of the device you still can't find in the controller list?
Are these devices set up with static IPs?
How are these devices connected, to the switch or to the EAP? Wired or wireless?

You can check if you can find them in the Insight list, delete them if you can and see if they will appear in the client list.

@ioannis.compet 

As I seen, there are many different reasons for the situation you mentioned, and it is especially important to know how these clients are connected to your network, so if you think it is a security risk to provide such information in the post, in my opinion, it is more advisable to contact tplink support directly, so that you can provide a more detailed topology diagram without any concerns, and it will be faster to locate and solve the problem lol.