There's no reason the OP shouldn't consolidate the loan into the mortgage and avail of the lower rates available, nor is there any reason she should be worse off in the long run as a result.
1. If the OP were to consolidate, however, she can realise the most substantial savings by continuing to pay at the current level thereby clearing the "top up" in the same time as the original loan, and, because the rates are lower, making a bigger dent in the outstanding mortgage balance as well.
2. If, on the other hand, her priority is to free up some money for day-to-day expenses, she could set the payment so that the top-up is paid off in the same timeframe as the original loan - but that will release some extra money since the rates available for mortgages are lower.
Points 1 & 2 elaborate a little on ClubMan's second last bullet point.
3. Finally, of course, it is an option to schedule the payment over the term of the full mortgage. This should generally be the least favoured option since it costs most over the lifetime of the loan. However, it's worth noting that the OP is going back to college and may have reduced income for some time and therefore quite reasonably want to leave the payments at the lowest amount possible [hopefully in anticipation of a higher income post-qualification].
Mortgage top-ups are not necessarily a bad thing, though they must be treated with caution. But it doesn't follow that people should avoid the savings they can make by borrowing at substantially lower rates. Used wisely, a mortgage top up can be a useful source of cheap funds. OTOH, of course, used foolishly it could risk the family home and the family's long term financial stability.