The Vivado IDE constraints manager saves any edited constraint back to its original location in the XDC files, but not in Tcl scripts. Any new constraint is saved at the end of the XDC file marked as target. In many cases, when your constraints set contains several XDC files, the target constraint file is not the last file in the list, and will not be loaded last when opening or reloading your design. As a consequence, the constraints sequence saved to constraint source files can be different from the one you had previously in memory.
Important: You must verify that the final sequence stored in the constraint files still works as expected. If you must modify the sequence, you must modify it by directly editing the constraint files. This is especially important for timing constraints.