The Vivado IDE constraints manager saves any edited constraints back to their original locations in the XDC files, but not in Tcl scripts. Any new constraint saves at the end of the XDC file marked as the target. When a constraint set has multiple XDC files, the target file often does not appear last in the list or load last. As a consequence, the sequence of constraints saved to the constraint source files can differ from the one you previously had in memory.
Important: Verify that the final
sequence stored in the constraint files works as expected. If you need to modify the
sequence, do so by directly editing the constraint files. This is especially important
for timing constraints.