Just as with a standard DFX design flow, Nested DFX design images should be checked using pr_verify to confirm all images are in sync. Like the core implementation tools (opt_design, etc.), pr_verify will act upon the design based on the current cells marked reconfigurable. With this in mind, perform apples-to-apples comparisons with the same current static design present.
In the examples shown here, run pr_verify to compare versions of A on a collection of checkpoints with only Top locked and cell A marked as reconfigurable - pr_recombine may be needed to create specific design images with this status. Run pr_verify on a collection of checkpoints with both Top and A1 locked to compare all images with different RMs for W and X, and then do the same with both Top and A2 locked to compare all images for Y and Z.