Have you restarted after you moved the fonts? I've had to do that in the past.
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Not sure if this is helpful or not, but we've had this same issue amongst the three of us in our art department for years. And the weird thing is, it's always a Helvetica Neu variant causing us trouble. I must have 55 versions of Helvetica Neu, and sure enough, my co-worker has 56, and it's that one that he used and I can't update.
We copied and deleted and installed and uninstalled and restarted and eventually, we just quit using the typeface. I know that's a bit extreme, but for us, it was a font we didn't care that much about and we just switched out to Avenir as our "house" face and the problem has pretty much gone away.
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The trouble with Helvetica and Helvetica Neue families is that there are a number of providers of these fonts with slightly different names — not just the external font names, but names within the font that applications and even the operating system use to find particular fonts.
In terms of 55 versus 56, those aren't version numbers for this font, but rather totally different styles of the font. At one time, it was quite popular to use numbers or combination of numbers to differentiate between different widths (condensed, semi-condensed, normal, expanded, etc.), italic or not, and thickness (ultra light through black).
FWIW, your solution of simply going to another font family (Avenir) with less complex naming issues seems reasonable (unless you absolutely, positively, must have Helvetica Neue)!