The modified DLLs provide extended functionality only, they do not and should not break compatiblity with other applications.
FlashFXP installs it's own modified version into the FlashFXP folder for a reason, unless you added FlashFXP to your search path there shouldnt be any problems.
Normally other applications will find the standard version in your windows folder.
Due to the fast pace of OpenSSL revisions it's common for developers to install a copy into their program folder, they know this version works with their software whereas a new version might cause compatiblity issues.
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