To generate such a script, launch SSDT and select Tools/SQL Server/New Schema Comparison.
Select your source and target databases.
Go into Settings and select only Indexes.
Run the comparison and script out the results. I suggest that you run this script in QA first, before risking affecting Production.
You will have to do this for every source/target database.
The absence of evidence is not evidence of absence.
Martin Rees
You can lead a horse to water, but a pencil must be lead.
Stan Laurel