First, you should confirm the problem actually exists. Within the lambda console, you can view the lambda's SHA256 BASE64 encoded hash. You can observe it before and after. As well, this SHA256 BASE64 encoded hash appears in CloudTrail when a lambda is created/updated.

Having said that and looking deeper, the contents of the zip file could be identical, but if it's zipped by different zipping software or even at different times, the SHA256 will almost certainly be different. Some zipping solutions (Such as Terraform's Archive provider) can produce exact ZIP files over and over, but others cannot.