Hi,
I have two schemas:
demo_rafal [let's say it's my DEV]
demo_rafal_test [my TEST]
Both schemas were created via the latest APEX 26.1
Oracle AI Database 26ai Enterprise Edition Release 23.26.2.2.0
(self-managed on OCI, not Autonomus)
sql /nolog
diff -source demo_rafal -target demo_rafal_test
Looks like all went well:

However, when trying to unzip the file, it looks like the zip file is empty

I reproduced the same steps on my Autonomous Database - all went well, no issues, and the zip is full of scripts.