The Curse Client and the WoWI Updater do try and overwrite each other on some addons. When I run my updates, I have them open side by side. Generally, they show the same version information number wise, but for whatever reason the one on WoWI would for instance say v2.02 and Curse will have it listed as 2.02
Unfortunately that "v" makes the other updater think its different, lol. Not a major deal, I just look at it and if the numbers are the same, it's all good
I haven't had any issue updating between the two udaters besides that.