Criminal Law advise

ONE FAMILY has complained against a PERSON.  That PERSON is neighbor of our ancestral home. My father had no direct professional contact with that PERSON. Just as a neighbor relation. They both had mobile nunber saved in their mobile. But that PERSON has committed some serious crime in a organized ways and seems to be the leader of group. Now police arrested that PERSON and now that ONE FAMILY has done FIR against that PERSON because they felt like they also may be victims of that PERSON crime. Now in this particular case that PERSON person is innocent (  this PERSON had not done any crime in this particular case other wise he is very very bad person). In this case that  PERSON had referred the FAMILY to my father for some work. Now as that PERSON is arrested in related work but for other persons work, that FAMILY is suspicious that PERSON may had wrong with them also, so they had done FIR and in investigation that PERSON said my father's name. But while interrogation that person also said that my father is innocent and have not having any connection with the crime. While interrogation my father the police is well convinced that my father is totally innocent and leave my father. But next they summoned my father and arrested him said that due to pressure from top officials and having direct contact with the PERSON and due to FIR from the FAMILY,the police had to do work as per law and taken my father in custody. The police had arrest 20-22 people in this crime. My father had no contact with any one except the PERSON. As this crime are serious. The judicial custody will be upto 90 days then only bail can be matter of right. Now the case is in Session Court. My father is in Judicial Custody for 20-25 days almost. Even the police are well convinced and said that there will be no problem if he innocent and assured us everything will be fine. Let police do their work everything will be ok. Now I have some questions. 1.As per my research, there is no time frame for submission of charge sheet, but if not submitting within 90 days ever one (20-22 including my father will get bail). But police will not give bail to everyone as they will flee to other state or county. Can 90 days remand be extended under any circumstances, if police unable to submit charge sheet? 2.As my father is totally innocent, and nobody is framing my father. And while investigating police no evidence of any wrong doing of my father. And all other witness in my father work place has said truth that my father is totally innocent. Even that PERSON also said my father is innocent. So no one expects the FAMILY is accusing my father. And one other thing the work done between my father and the FAMILY is totally legally documented.Even the document are not sighed by my father. Documents sighed by higher officials of my father. Everything is in good manner and no crime done. Even police after verification said everything in this office is right manner nothing to worry. 3.If no material evidence found against my father and no witnesses against my father,Can police file charge sheet against my father? 4.Without evidence can police charge sheet? 5.Can name be completely removed from charge sheet? 6.After charge sheet submitted and  no evidence found against my father, let's say according to charge sheet,my father is innocent. After how many days of submission of charge sheet, court will say my father is innocent? 7.Is it really possible to remove the name of person from charge sheet if no evidence found?