If Alfred Dreyfus was innocent and the people in the general staff knew it, why did they try to cover it up and protect the guilty man? Weren't they concerned that there was still a mole present?
The short answer is that we do not know for certain.
The most likely answer, and the one that has gained consensus with most historians, is simply that the French high command considered that its own credibility was bound up with upholding the earlier conviction of Dreyfus. This was despite the fact that within a year the high command already had evidence that Dreyfus was innocent.
However, it has been suggested (without any actual evidence to support it) that Ferdinand Walsin Esterhazy, who is believed to have been the actual spy in that case, was actually a double-agent working with French counter-intelligence.
The details of the Dreyfus Affair are covered in some detail on the Wikipedia page. In short, Dreyfus, was arrested for treason on 15 October 1894 and summarily convicted by a secret court martial 5 January 1895.
Picquart was then relieved of duty with the Deuxième Bureau, and transferred to command the 4th Regiment of Tirailleurs in the southern desert of Tunisia in November 1896, presumably to prevent him from going public with that evidence.
Esterhazy was found not guilty by a secret court martial in 1898. He then left France for England.
Dreyfus's was given a second trial in 1899. He was declared guilty of treason again, despite evidence of his innocence.
Dreyfus was pardoned by President Émile Loubet in 1899, but it wasn't until 12 July 1906 that Dreyfus was officially exonerated by a military commission.
To the best of my knowledge, if the records of the secret courts martial survive, they have never been made public. However, if you are interested in taking your research further, the secret military file of the Dreyfus Affair (Le dossier secret de l'affaire Dreyfus), which contains many documents pertaining to the Dreyfus Affair, had been digitised and made available online by the Historical Department of the French Ministry of Defence (Service Historique de la Défense).