If I have a Vigor in play, as well as Hardened Scales, and say someone cast Lightning Bolt on one of my other creatures. Vigor's text says "for each 1 damage prevented", so is that three separate events (one for each point of damage), which Hardened Scales can pump by one each (so the affected creature would get six +1/+1 counters)? Or is that only one replacement effect, which Hardened Scales can only pump once (so the affected creature would get four +1/+1 counters)?
"For each 1 damage" is just a variable, not an instruction to be performed multiple times. Replacement effects can replace each other, just not themselves. In this case, Vigor sees a damage-dealing event to replace with placing +1/+1 counters, which are placed all at once. That's replaced by the Scales with placing the additional counter. All in all that's a total of four +1/+1 counters.
I̟̥͍̠ͅn̩͉̣͍̬͚ͅ ̬̬͖t̯̹̞̺͖͓̯̤h̘͍̬e͙̯͈̖̼̮ ̭̬f̺̲̲̪i͙͉̟̩̰r̪̝͚͈̝̥͍̝̲s̼̻͇̘̳͔ͅt̲̺̳̗̜̪̙ ̳̺̥̻͚̗ͅm̜̜̟̰͈͓͎͇o̝̖̮̝͇m̯̻̞̼̫̗͓̤e̩̯̬̮̩n͎̱̪̲̹͖t͇̖s̰̮ͅ,̤̲͙̻̭̻̯̹̰ ̖t̫̙̺̯͖͚̯ͅh͙̯̦̳̗̰̟e͖̪͉̼̯ ̪͕g̞̣͔a̗̦t̬̬͓͙̫̖̭̻e̩̻̯ ̜̖̦̖̤̭͙̬t̞̹̥̪͎͉ͅo͕͚͍͇̲͇͓̺ ̭̬͙͈̣̻t͈͍͙͓̫̖͙̩h̪̬̖̙e̗͈ ̗̬̟̞̺̤͉̯ͅa̦̯͚̙̜̮f͉͙̲̣̞̼t̪̤̞̣͚e̲͉̳̥r͇̪̙͚͓l̥̞̞͎̹̯̹ͅi͓̬f̮̥̬̞͈ͅe͎ ̟̩̤̳̠̯̩̯o̮̘̲p̟͚̣̞͉͓e͍̩̣n͔̼͕͚̜e̬̱d̼̘͎̖̹͍̮̠,͖̺̭̱̮ ̣̲͖̬̪̭̥a̪͚n̟̲̝̤̤̞̗d̘̱̗͇̮͕̳͕͔ ͖̞͉͎t̹̙͎h̰̱͉̗e̪̞̱̝̹̩ͅ ̠̱̩̭̦p̯̙e͓o̳͚̰̯̺̱̰͔̘p̬͎̱̣̼̩͇l̗̟̖͚̠e̱͉͔̱̦̬̟̙ ̖͚̪͔̼̦w̺̖̤̱e͖̗̻̦͓̖̘̜r̭̥e͔̹̫̱͕̦̰͕ ̗͔̠p̠̗͍͍̱̳̠r̰͔͎̰o͉̥͓̰͚̥s̟͚̹̱͔̣t͉̙̳̖͖̪̮r̥̘̥͙̹a͉̟̫̟̳̠̟̭t͈̜̰͈͎e̞̣̭̲̬ ͚̗̯̟͙i͍͖̰̘̦͖͉ṇ̮̻̯̦̲̩͍ ̦̮͚̫̤t͉͖̫͕ͅͅh͙̮̻̘̣̮̼e͕̺ ͙l͕̠͎̰̥i̲͓͉̲g̫̳̟͈͇̖h̠̦̖t͓̯͎̗ ̳̪̘̟̙̩̦o̫̲f̙͔̰̙̠ ̹̪̗͇̯t͖̼̼͉͖̬h̹͇̩e͚̖̺̤͉̹͕̪ ͚͓̭̝̺G͎̗̯̩o̫̯̮̟̮̳̘d̜̲͙̠-̩̳̯̲̗̜P̹̘̥͉̝h͍͈̗̖̝ͅa͍̗̮̼̗r̜̖͇̙̺a̭̺͔̞̳͈o̪̣͓̯̬͙̯̰̗h̖̦͈̥̯͔.͇̣̙̝