It appears so. I have multiple copies of the same article in some cases and the pre-Calibre ones work fine, typical snags in lines breaks and the such, but readable. In addition, I can highlight the old pdfs but not the new ones.
I'm afraid I was not systematic in consolidating my library, so I can't say for sure the history of each file, but when it comes to journal articles I always access them the same way. Even if the same article had been downloaded multiple times instead of duplicated, there shouldn't be format differences. Unless there's something happening in the way the file is downloaded (can we blame this all on Google Chrome, which I switched to around the same time?).
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