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After your patent application had been submitted do not waste time. You can label your invention as patent pending and start marketing it.

And

After your patent application has been submitted do not waste time. You can label your invention as patent pending and start marketing it.

Are both useable? They seem to mean the same thing here. Is the past perfect unnecessary?
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In this context you can only use "has been" since the use is present perfect tense, not past perfect. You can tell from the present instruction "do not waste time" as well as the following sentence "you can label...and start marketing" that the context is in the present not past. Therefore, you would use "has been" not "had been."

Just to explain the difference:

Present perfect tense describes an action that happened at an indefinite time in the past or that began in the past and continues in the present.This tense is formed by using has/have with the past participle of the verb.

Past perfect tense describes an action that took place in the past before another past action. This tense is formed by using had with the past participle of the verb.

In this context you have continuing action and no other past action.
Comments  
In this context you would use "has been" since the use is actually present perfect tense, not past perfect. The present tense instruction "do not waste time" and the following sentence "you can label...and start marketing..." mean the context is in the present not past. So you can only use "has" not "had."
 KJinCali79's reply was promoted to an answer.