Last night we defeated Nyogtha after the doom track filled up, but I am not sure if we played against him correctly. My players were under the impression that they could use clue tokens to reroll if they failed a check against him to prevent getting devoured. Against Nyogtha, the first player must roll a die and get a success (5 or 6) or be devoured. My players used their blessing cards to succeed on a 4, 5 or 6 AND they used clue tokens to reroll if they failed. Does that sound right to you?

This is a question which has been asked before ~ not necessarily regarding Nyogtha, but other such situations.  Whenever an Investigator rolls a Skill Check, they may certainly use clue Tokens should the result produce a failure (or you need to produce more successes than those generated by the original roll).  There are alos rolls, such as those generated when determining whether or not an Investigator retains or discards a Curse or B;essing, a Retainer, etc.  These are not Skill Checks and the player may not use a Clue Token. 

However, success is defined differently if the Investigator is either Blessed or Cursed.

Also, people quite frequently misunderstand what a clue token does.  Spending a clue token does not allow you to re-roll a die.  It allows you to add a bonus die to your skill check.  So, since Nyogtha's attack calls for the 1st player to simply roll a die, this is not a skill check; you just roll 1 die.  Clue tokens can not be spent on Nyogtha's attack.  However, blessings and curses still affect what is considered a success, even during Nyogtha's attack.  So you were half right.