Funds made available on types of checks that must be given next day availability by Reg CC (cashiers checks, govt checks, etc...) do not count toward the $100 that must be made available next day on check deposits. See commentary on 229.10:
b. The $100 that must be made available under this rule is in addition to the amount that must be made available for withdrawal on the business day after deposit under other provisions of this section. For example, if a customer deposits a $1,000 Treasury check, and a $1,000 local check in its account on Monday, $1,100 must be made available for
withdrawal on Tuesday--the proceeds of the $1,000 Treasury check, as well as the first $100 of the local check.
So for the $100 rule, you need to total all checks deposited on a business day that ARE NOT subject to next day availability by rule and make $100 of that total available.
In your question you ask:
If we have a customer deposit let's say three different checks and we apply a hold to only one of the checks, do we need to give an additional $100 next day availability to the one check we hold funds on?
If the two checks you don't hold total at least $100 and are not checks that you have to make available next day by law, then you don't need to release additional funds.
_________________________
Opinions are not necessarily those of my employer and should not be construed as legal advice.