The implication was a bit more than vague - Wells was talking about Tess, then tells Joe that he is "one of the few people I know that truly understands that kind of loss," and then refers to Iris's mother, and how Wells and Joe are "members of a rather exclusive club, I suppose. One who's membership is too expensive."
I don't think when he refers to "loss" he's talking about "your wife left with the mailman" levels of loss.
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If Flash really changed his own history that dramatically, then there's no reason for her to be in sisterly mode, since RF never killed Barry's mother or framed his father (seeing as he never existed), so she would have grown up as the 'girl next door' and his childhood sweetheart, rather than the 'girl down the hall' and his foster sister.
Plus, Eddie's past wasn't changed, so I'm not sure that him being sucked into the wormhole would have erased him from history anyway.