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Ok, I'm not an expert.
1) So long as calibre finds your library, it doesn't matter which version of the program you use. Being on an external hard disk does not matter in this situation. Even if you move the drive to another computer, you'll just have to install calibre on that system and set the drive path to your library. Once it knows where the library is located, calibre will operate correctly thereafter.
2) Absolutely not. There is no default connection between Flash and calibre. Any such connection is one that you would have had to make by hand, yourself.
Both calibre and flashplayer can use a lot of memory and/or processing time when operating. So if they're both working on separate projects, but at the same time (you're multi-tasking), that could account for the slow down. But that should be a relatively short period (minutes to hours, worst case, but not days).
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