The information in the files isn't going to be forgotton no matter how fervently you wish it would. No conclusions were reached and no-one was ruled out at the end of the first investigation.
There was no first investigation if your reference is to the one led by Amaral. The first investigation started in May 2007 ended with the archiving dispatch of 2008.
Amaral was sacked from the investigation and Almeida the author of the interim report in the PJ files left shortly thereafter leaving the threads to be picked up by Rebelo and his highly competent and perfectly qualified team for such an investigation.
Continuing on from what had gone on before ... the Rebelo team found there was no evidence and never had been which justified the path taken by their predecessors.
If there had been they would have continued on that path and invited Kate and Gerry back to Portugal ... which as arguidos they could not refuse to do ... and taken the process forward from there.
There was no evidence and never had been to justify that course of action. What evidence there was exonerated them ... which is why the public prosecutors said in effect that they never should have been made suspects in the first instance.
The tragedy of all this is that while police time and resources had been misdirected the focus of the police work on Madeleine was lost and goodness knows what initiatives on her behalf were missed.
I think the classic one being the time and effort spent analysing the phone traffic of the victims but apparently entirely ignoring phone traffic between burglars until it was taken up for investigation by Scotland Yard many years down the line.