Deleting duplicate games in SCID is not as straight forward as it may seem and the process is not explain in the help file. Here's how to do.
1- Open the database with duplicates
Always have the Database Switcher and the Games List tabs open as well.
2- Open the maintenance window (Ctrl+M)
3- In the Database operations section, click on Delete twin games... this will open the following window:
Check the criteria that suit your database best.
In the Examine which games section select All games in DB.
In the When deleting twin games section, uncheck all but Set filter to all deleted twin games. This way after marking twin games for deletion, you can see what games SCID selected in the Games List tab.
Now click the Delete Games button and then "yes" if a popup appears.
4- A new window pops up, the Twin games checker with the pairs of games selected. 1 is checked as deleted (delete flag), the other is not.
If you don't have too many duplicates, it's a good thing to take a look at what SCID selected by clicking on the Next pair button. This windows works in parallel with the filtered Games List tab.
5- If in the Twin games check window you see both games are checked or unchecked, it means your filters (deletion criteria) didn't work well.
Go through all the pairs and check at least 1 game.
An easier way is to take a look at the filtered Games List tab and check for duplicates. Select one and right click on it -> remove from filter. I usually never use the Twin games checker and close it as soon as it pops up.
The games removed from the filter will not be deleted.
6- Back to the maintenance window
In the Delete flag section, click on Delete filter games.
The games will not be deleted yet! Only confirmed as "to be deleted"...
7- To finally delete the games you need to click on the Compact database button in the Database operations section.
This will bring a window with the state of your database after compacting it.
If this looks good to you, click on Compact game file to finally delete the duplicates (and make your DB smaller additionally). When done you can go to the DB switcher tab and right click on your database to reset the filter. (at the moment it should show 0/x games displaying)
If you're not happy with this or unsure about what you did, click cancel and go back to the DB maintenance window. There, click on Undelete all to unmark all deleted games and be back to normal.