Serial Number is one of the criterion used in the Identification Rules that come out of the box, so if Discovery sees a Server in your estate with no Serial Number and pulls that information back, then it is going to create a new entry in the CMDB if it cannot match with an existing Server.
Note that these Identification Rules that come out of the box are inherited all the way down from the Hardware Class, so it might be prudent to start thinking of ones that are specific to your Server Classes to account for the nature of your environment.
The bigger question here is why is the Serial Number attribute disappearing for your Servers, you will want to chat to your Network Team about that. The outcome of that conversation might mean that you need to think about alternative Identifier criterion.
In the meantime, if you want to avoid CIs getting created without a Serial Number then you can create an IRE Data Source Rule to block the insert of any Windows or Linux Server that tries to enter the CMDB without a Serial Number.
