This question pertains to Facility maintenance. Lets assume a university with close to 1000 buildings. Facility condition assessments are performed. System deficiencies are identified. There is also a CMMS product.
>> what is the best way to "close the loop" and link these two?

I guess you have to enter the findings of the assessment into the CMMS. Then they are linked.

WQe had many external reports written and enter the findings into CMMS for actions to be taken.

Josh - I like your answer (keeping the deficiencies inside the CMMS product). I would then link them perhaps on a system-subsystem code field.
I should point out that there are facility (software) vendors who promote their product for Deficiency tracking.... but I have always asked myself ... Why?
I can tailor the base CMMS product to accomodate any details that they would have.
w/br
j.r.