Keep Transformations in the Replace Clone dialogue enables you to keep any changes (such as scale, resize, flip, rotation, etc.) that may have been applied to a specific object while still allowing you to apply changes to all of your clones. Try this example:
1. Create a new Drawing document.
2. Open the Animals Library.
3. Drag the Cow to the document three times.
4. Change the first cow by resizing it.
5. Change the second cow by filling it with the color green.
6. Select the second cow with the arrow tool.
7. Choose Replace Clones... from the Edit menu.
8. Click on the button Use Selected.
9. Click Replace All.
Notice what happens. Since the Keep Transformations box is checked, the first cow stays resized but is changed to the color green. The third cow is also changed to green.
Now try the same nine steps above, but uncheck the Keep Transformation box. Notice that all the cows are all the same size and green.