Desaparecidas las causas o motivos que hubiesen dado lugar a cualquier retención,

Having no further cause or motive that may have given raise to any....
With the absence of any cause or motive that may have given raise to any....

'...with any possible grounds or reasons which may have given rise to the withholding any amount having subsided,..'

Hello again, Lydianette,

Here's is my suggestion, and I'll once again guide you through my thought process:

"desaparecidas" means that there were reasons for withholding payment from the Contractor but those reasons now cease to exist. Therefore I'd simply use "cessation." The provision states that payment must be made immediately following such cessation, so I would use --> "Upon cessation"

"Causas" and "motivos" are commonly translated as grounds or reasons. They form the basis for the withholding of payment.

My full translation would be:

"Upon cessation of the grounds or reasons forming the basis for the withholding of any amount, the amount shall be duly paid."

Alternatively, a less literal version:
"Any amount withheld on the basis of grounds or reasons that cease to exist shall be duly paid upon the cessation thereof."

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Note added at 1 hr (2018-02-02 19:03:42 GMT)
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In response to Robert Carter's (understandable) concern with the use of "cessation:" it's true that we commonly see the term used in conjunction with "to exist" as in e.g., a company that "ceases to exist." But the plain meaning of "cessation" is "ending/being brought to an end." In this case, we're dealing with specific circumstances (e.g. defective works not timely remedied, status of default on contractual payments) that must be brought to an end (i.e. that must cease) in order for the payment to be returned. So what ceases are the circumstances. Now, if we were referring to the cessation of a company, a body, or let's say documents that were destroyed in a fire, we'd use "cease to exist." Hope this clears it up, Robert and anybody else interested.

From the context, it appears that the reasons for withholding payment may be temporary and once action is taken to remedy the defects, contractor will receive payment withheld in full.