Regarding fteqcc, you need -TH2 on the commandline so that it knows its meant to accept hexenc keywords and to use the hexen2 opcodes+crc rules (if you're using the gui version, there's a checkbox in the options menu).
Alternatively, you can also place '#pragma TARGET H2' and '#pragma keyword enable thinktime' at the top of whichever hc file is the first to compile.
Without doing one of those things, fteqcc will assume you're compiling for quake.
Regarding hcc, you should probably use a version from
http://uhexen2.sourceforge.net/ and indeed you should definitely grab the gamecode source from that site instead of other versions. The vanilla hexenc code is riddled with bugs, hopefully the HoT version will have the more noticable bugs fixed, or at least hidden.
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