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This is actually a problem with the Curse Client. It keeps its own records about which versions of addons it thinks you have. This is why it reinstalls every addon the first time you use it -- it does not look at the TOC version field, but rather updates an internal database each time you use the Curse Client to download an update.
So, even though you updated AddonX from Version2 to Version3 with the Minion, since the last version the Curse Client downloaded was Version2, it thinks it needs to download Version3 to get you up to date, completely unaware that you've already done this by some other means.
Your best bet is to either (a) just let the Curse Client download duplicate updates, or (b) go through each addon that appears on both sites, figure out which on the author updates most frequently (or provides more prompt support, or whatever) and tell the other site's client to ignore the addon.
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