I think it’ll be hard to group the two buildings together into one ISEC. The student body by and large refers to the first building solely as ISEC. It’ll be very hard to remove that association, IMO. Sort of like a John Hancock/200 Clarendon or Willis/Sears Tower issue.
Building name norms usually change over pretty quickly in student bodies, since most students usually only hang around for 4 years. Whether or not ISEC will continue to stick with students depends on if they keep the name with the donor's name (i.e. 'John Smith Interdisciplinary Science and Engineering Complex vs. Smith Hall/Center,') and that may continue to stick as ISEC. These interdisciplinary science/engineering centers are strong selling points for admissions, donors, and general PR, so they may likely keep it to keep up with BU's EPIC, MIT.NANO, Harvard SEC, etc.
Also peculiar: It's unclear on the Naming Opportunities page if the building will be named something other than ISEC. They have plenty of other donor opportunities (the atrium and spiral stairs for $3m, auditorium for $3m, a research floor for $2.5m, meeting spaces for $100k-250k each, etc.). Naming the building is listed as an option, but there's no 'more info' like the other opportunities. I'm sure if someone showed up with enough money, they'd rename it after them, and the school would push that name in respect of the donor.