Assuming you don't want to keep anything from the old version (I'm not sure if there are unique items where you would want to anyway), can you just remove the old version, do a repair all, then add the new version? A little simpler I guess.
Your method will temporarily change load order (-1 shift) for mods below the one you are updating. MCP code loading order fixes and/or Mash Repair All could be able to fix problems, or not.
I think if mods have different names using a Mash replacer (correct procedure below) is safer for mods loading after the one you are updating.
Spoiler (1) Ensure names of old version of mod and new version are different.
(2) Copy new version into Data Files
(3) On Mash's mods tab change load order so new version is right next to old version.
(4) On Mash's mods tab right click NEW version and choose Updaters
(5) Select OLD version of mod, Mash lets me know if my save game needs updating
(6) If it does head on over to the Saves tab and select appropriate save
(7) Right click the old version in the list of mods associated with the save game and choose Change to...
(8) Select new version of mod
(9) Click Save
(10) Back onto the Mods tab and deselect the old version and select the new version
(11) Delete old version from Data Files
(12) For completeness, run a Repair All against the save game
Or, If you want to start the mod anew, replace the mod with a dummy empty one with same timestamp, load, save, replace the dummy with the new version of mod. This way load order is not changed, it seems less risky for me.
Mash has been engineered before MCP was available, and nobody knows exactly how/how well various Mash procedures interact with MCP loading fixes, so it may be they work in perfect harmony, or not.