I wonder if it is grammatically fine to use two
have/has been in the same sentence?
After you have been informed that your paper has been accepted…
The sentence is grammatically fine. There could be two "has/ have been" in a sentence. Grammar does not prohibit this.
These clauses are in passivised present perfect. Without the main clause, it cannot be decisively told whether the sentence is correct or not. However from the '...' we may safely presume that that there is a satisfactory princpal clause that brings this sentence to its logical ending.
It is often hotly argued against too much use of passive but uptill now those two subordinate adverb and noun clauses in passive present perfect are fine provided...!!