Here's a trick for working with two different found sets without operations on one changing the other even when they are both from the same table:
Open Manage | Database | Relationships
Click on a Table Occurrence box for that table to select it, then click the button with two green plus signs to make a new table occurrence of the same table.
Now click OK to leave Manage | Database and create a new layout to this new table occurrence. (Select the name of the new occurrence from the "show records from" drop down.
Now your scripts (or if you do this by hand) can perform finds, sort records, omit records, etc. with one layout selected and these operations won't change what records are present in the found set on the other layout. So your script can freeze the window, change layouts perform the find, then do whatever else you need with this data and then switch back to your original layout where it's found set, current record, etc. will remain unchanged.
Note: This can also be done without the extra table occurrence and layout, if you open a new window and do the operations on the same layout, but within the new window. This can be a bit trickier, however, if you are using windows, as the new window command can trigger an unwanted resize of the original window if the user is working with the database with the windows maximized. Using two layouts with different table occurrences avoids that issue.