You can use -filemask switch to exclude specific subfolders:
https://beta.winscp.net/eng/docs/scriptcommand_synchronize#filemask

I need to create an automatic script in order to deploy my app automatically.
I want define custom folders to check and I want to exclude others folders to analyze
Could you please help me to understand?

An example:

open ftp://username:[email protected]/

synchronize -preview remote
C:\projects\myProject
/myDomain.com
C:\projects\myProject\subfoder1;
C:\projects\myProject\subfolder2
|
C:\projects\myProject
\subfoderToExclude;

exit