Yes, that should be no problem. You should first check if any packages has to be installed, for the detaild info see release notes:
http://www.howtoforge.com/forums/showthread.php?t=47925
And if the perfect server guide for your operating system version contains some instructions to edit the stdio.h file, then make sure that you have edited the file before you update or the apache compilation may fail.
Before you update, always make a backup of the directories /root/ispconfig and /home/admispconfig and the ispconfig mysql database so you can switch back if a update fails.
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