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According to Unison Manual, using -force <root>:

Including the preference -force root causes Unison to resolve all differences (even non-conflicting changes) in favor of root.

However, I want to force it only in conflicting changes, how can I do it?

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I found my answer just after posting, but I would like to keep it here for other people looking into the same problem:

In those cases, you should use "-prefer" instead of "-force" :

Including the preference -prefer root causes Unison always to resolve conflicts in favor of root, rather than asking for guidance from the user. (The syntax of root is the same as for the root preference, plus the special values newer and older.)

That's all :)

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