(disclaimer: I work at Unity)
It is a button toggle problem, if the code does not do nasty things (like casting between a pointer and a 4-byte-integer -> all works until pointers are not 4 bytes). Or if a code depends on, for example, inline assembly (VisualC++ remove that in 64 bit). Or if the code generates code at runtime, for example JavaScript engines - for 64 bit they need to generate different code.
In Unity's case, the biggest holdup, of all things, was WebKit (used for asset store window & some other things). Turns out, there's no 64 bit webkit for Windows (or there wasn't a while ago). We had to replace Webkit with Gecko, which was quite involved task.
