I did a lot of research on Bourrienne when I was working on my dissertation in Bremen and Hamburg. Specifically, I wanted to know exactly how did Bourrienne get rich, and then of course: did he in fact give any of it back?
There is plenty of evidence for the former. A lot of testimony in the Staatarchiv Hamburg from people making claims afterwards, or recalling how Bourrienne blackmailed them (i.e., pay him, or he'll have you arrested for smuggling... whether you are or not.)
There is, however, no evidence for the latter. I never found a single example of Bourrienne ever "giving it back" to anybody.
Which, of course, makes sense. How could he? Extortion and corruption isn't exactly the sort of thing that one keeps a log or record of. It's not as if he could have everybody line up and present him with their receipts to reclaim this or that. It was long gone, and there wasn't much of a paper trail in any event.
So I'd be astonished if Bourrienne ever gave anything back to anybody.
To my mind, this is one of those things that surely Napoleon knew better about; it's so obvious to even the most casual mind, that he must have known that a corrupt official who had been extorting people for years, couldn't possibly "give it back." Thus his alleged order* for Bourrienne to do so, I suspect, can only be seen as an attempt at P.R., like his alleged "discouraging" of plundering by the marshals or generals. Or his tolerance of Fouché's and Talleyrand's corruption, the bribes run by Josephine and Reinhard, the acceptance of bribes by douanes, consuls, and other local authorities like Bourrienne. Just literally today, in fact, I came across an example:
When the French turned over Hannover to the Prussians in Autumn 1805, there was an awkward moment regarding the little fortress of Hameln, in which the French garrison commander, Barbou, claimed that Napoleon had ordered him to stay until he had collected the last of the overdue French contributions (1.2mil) - that's the money the French demanded from the local civilians for the maintenance of the French garrisons. Barbou had accepted a personal bribe (a "gratification") of 100,000 francs, as had Rapp, during his tenure there, to look the other way, but now he was on the spot from Napoleon (or so he claimed.) The French eventually settled for 800,000, part of which was paid by Prussia. The Prussians informed Napoleon that both Barbou and Rapp had taken bribes, but to my knowledge nothing was ever done about it.
So, given the extraordinarily high number of highly-placed people in the Empire who were corrupt, either Napoleon is not in control (which I doubt very much), or he is OK with it, which is the only logical conclusion.
* I write "alleged" because I haven't actually seen the order from Napoleon to Bourrienne, in which he tells B. to give "half" of it back. If anybody has the exact original text, I'd love to see it.