I'll try to answer as best as I can, I apologize for the wordiness. I am not a lawyer and none of this is not legal advice. Different universities will have different policies, and different legal jurisdictions (for example Nebraska is in the 8th appellate circuit, and I live in the 6th circuit) may have different legal guidelines to follow unless something has been superseded by SCOTUS.
First of all, the Title IX regulations were entirely rewritten by DeVos's Dept of Ed last year, and all universities had to be compliant in pretty short order. I have a lot of problems with the new regs, but one of the impacts is that Title IX processes are now in favor of the Respondent (the accused party), as the investigative and hearing process is more complicated, and more like a courtroom setting, and will have the effect of deterring Complainants from coming forward. So depending on when this particular complaint occurred (before August 2020 or after), the process may be different.
In any event, I would not have expected Boy to be suspended during the investigation unless there was some reasonable belief that his continued presence on campus posed a serious risk to himself, the Complainant, or the community. Generally speaking, we don't take punitive action against without finding them responsible for a policy violation first, which requires the investigation and then the hearing. There are often other accommodations that can be made during the investigation (such as rearranging schedules, temporarily and voluntarily moving someone if they are in a residence hall, and/or mutual no contact orders). For the sake of due process, the Complainant and the Respondent need to be treated fairly throughout the process, and hopefully not have either of their academic opportunities disrupted. So for him to be suspended during the investigation, there must have been some sort of valid concern that he was still a threat, and that decision was hopefully very heavily scrutinized.
So, if he was found to not be responsible, I hope that he was immediately reinstated. The impact of his suspension very well could have harmed his academic pursuits. I would not expect the full investigation to go into his file, though. At my university, I know that in employee-related cases, the only thing that ever shows up in an employee's personnel file is a disciplinary letter only if the investigation results in a finding and it goes to hearing. My investigative reports are sent to the parties who need to know, but the report itself is typically not part of the file. I don't dig into student conduct files as often, but I believe that the only thing that ends up in the files where I work is the disposition (the final results) of the case, and not the investigative report itself. That report and the evidence is stored elsewhere. Boy should have the right to view his file, so maybe he should ask, to see what is in there.
My school's policies do have provisions against knowingly providing false information at any part of the process. It is a violation of policy and can similarly be investigated and result in discipline. However, things like that are very hard to prove. If a complaint is made in good faith but the evidence is not sufficient to support it, that is not necessarily a false report. Proving that the report was knowingly false is very, very hard, and this complaint might even be construed to be retaliatory. Of course, retaliation is also a violation of policy. So I would guess that he could file a complaint himself, he would be hard pressed to have sufficient evidence to support it.
That is always a possibility of course. In my investigations, I work really hard to treat all parties with respect, dignity, and empathy. You get more flies with honey than with vinegar, they say. But that doesn't mean that the process won't be intimidating or just flat out suck for all of the people involved. But there are multiple levels in the process. A student complaint starts with resources and support services offered by a Deputy Title IX Coordinator, then it goes to an investigator if the allegations are serious enough, then if a hearing is appropriate the case goes to a hearing panel who makes the actual decisions in the case, and there are appeal processes for both the investigation and the hearing if there is an error along the way. If it still doesn't go well, the parties always have the right to file a lawsuit. So everyone involved has a strong interest in getting it right.
Hell, I even once investigated a discrimination complaint against a Title IX investigator in our student conduct office across campus. The complainant accused the investigator of being an a$$hole, and racist to boot (which is why it came to me), so I carefully examined the investigative process that the other office used. There is always another step, and everyone who gets into this line of work has a strong sense of justice. But there has to be plenty of evidence in order to get anywhere.