I don’t know if she can be removed from ballots once nominated.
Does anyone know if they can change candidates once they nominate one?
All that said, why would they substitute in someone else? Someone being indicted by a grand jury? Isn't that par for the course for most Democrats to begin with? And you know the Dixie Mafia would drag Obama out of the WH by his big ears to do an executive pardon for Hillary (brushing off the crimes as ‘politically motivated witch hunt’ since, well, rules only apply to conservatives.)
I don't know for certain, but I'm guessing there must be a way to do it. For example (speaking in general terms now, not Hillary) suppose a candidate were to be nominated, then suffered a stroke and was obviously in no condition to continue to run for the office. There has to be a way to replace that nominee.
Generally, state laws require that candidates on the general election ballot be formally nominated by their political party’s national convention held in a presidential election year. The laws vary by state.
So theoretically, the Dems could re-open their national convention and have the delegates nominate a replacement. Whether or not their party rules allow for such a process is another story. There could also be state laws that require the nominee’s name to have been on a primary ballot or to have been selected by party caucus.
Another limitation would be state deadlines for political parties to submit the names of their nominees to the SOS for placement on the general election ballots. Typically, it’s at least 60 days before the general election. Sometimes more.