As you mentioned, changing the limits via the admin module is easy.
Changing quota definitions has a bigger impact. There is no quota "re-align" feature that changes the quota data from the old to the new. Yes, it would be nice.
In situations like this, I tend to backup the data now, think about the affects of the quota changes, make those changes and then continue surveying.
Thinking of your new quotas, manually calculate the completed counts in the current data set (you will also need to consider potential completes that currently reside as incompletes) and then set your new quota targets and definitions up. Now continue the surveying.
This gets that more difficult when least fill quotas are involved or there are many quotas involved.
Apologies for not being the bearer of good news.