I'm pretty sure the no more than 48 units of Level I rule is still applicable. They may simply have written it somewhere else in the calendar.
If you can find where it was written in previous years, I can try to find the equivalent in this year's.
However, in general, I have been told by the Department of Biology at least, that if rules change in succeeding years, you are allowed to follow either year, whichever is easier (something along those lines). For example, in previous years, Honours Biology students were required to take all the second year biology courses (I think so anyway...) but now you are only required to take 3 of them, so you are allowed to follow the latter even if you started the program before the change was made.
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EDIT:
I found it:
http://registrar.mcmaster.ca /CALEN...ent/pg121.html
"
Limit on Level I Courses: In most Faculties, you may not obtain credit in more than 42 units of Level I courses in a three-level program, or more than 48 units in a four-level program. "