Serial.Event() only runs once (using single char input) - serialization

Question

On my Arduino Mega 2560, I'm trying to run a motor that turns a 20-vial container (accepting int input 1-20) while regulating temperature via PID of a separate cooler. I am generally new to this field of technology so bear with me. I also have an interrupt set up for an encoder to keep track of vial position.
The void serialEvent() and void loop() are the most important portions to look at, but I decided to put the rest of the code in there just in case you needed to see it.
#include <PID_v1.h>
#include <SPI.h>
#include <TMC26XStepper.h>
#define COOL_INPUT 0
#define PIN_OUTPUT 9
TMC26XStepper tmc26XStepper = TMC26XStepper(200,5,7,6,500);
int step = 6;
int value;
int i;
char junk = ' ';
volatile long enc_count = 0;
const byte interruptPinA = 2;
const byte interruptPinB = 3;
//Define Variables we'll be connecting to
int outMax = 255;
int outMin = -145;
double Setpoint, Input, Output;
double heatInput, heatOutput, originalInput;
//Specify the links and initial tuning parameters
// AGGRESSIVE VALUES (to get to 4 deg C)
double aggKp=8.0, aggKi=3.0, aggKd=0.15;
// CONSERVATIVE VALUES (to hover around 4 deg C)
double consKp=2.5, consKi = 0.0, consKd = 1.0;
PID myPID(&Input, &Output, &Setpoint, aggKp, aggKi, aggKd, REVERSE);
void setup()
{
pinMode(step, OUTPUT);
pinMode(interruptPinA, INPUT_PULLUP);
pinMode(interruptPinB, INPUT_PULLUP);
attachInterrupt(digitalPinToInterrupt(interruptPinA), encoder_isr, CHANGE);
attachInterrupt(digitalPinToInterrupt(interruptPinB), encoder_isr, CHANGE);
//initialize the variables we're linked to
Input = (5.0*analogRead(COOL_INPUT)*100.0) / 1024;
Setpoint = 10.75;
myPID.SetOutputLimits(outMin, outMax);
//turn the PID on
myPID.SetMode(AUTOMATIC);
Serial.begin(115200);
tmc26XStepper.setSpreadCycleChopper(2,24,8,6,0);
tmc26XStepper.setMicrosteps(32);
tmc26XStepper.setStallGuardThreshold(4,0);
Serial.println("...started...");
tmc26XStepper.start();
Serial.flush();
Serial.println("Enter vial numbers 1-20");
}
void loop() {
Input = (5.0*analogRead(COOL_INPUT)*100.0) / 1024;
// A BUNCH OF CODE FOR TEMP REGULATION
Serial.println(Input);
delay(150);
}
void serialEvent() {
while (Serial.available() == 0) {}
i = Serial.parseInt();
Serial.print("position: ");
Serial.print(i);
Serial.print(" ");
while (Serial.available() > 0) {
junk = Serial.read();
}
if (i == 1) {
value = 0;
} else {
int num = i - 1;
value = num * 72;
}
while (enc_count != value) {
digitalWrite(6, HIGH);
delayMicroseconds(100);
digitalWrite(6, LOW);
delayMicroseconds(100);
if (enc_count == 1440) {
enc_count = 0;
}
}
Serial.println(enc_count);
}
// INFO FOR ENCODER
void encoder_isr() {
static int8_t lookup_table[] = {0,-1,1,0,1,0,0,-1,-1,0,0,1,0,1,-1,0};
static uint8_t enc_val = 0;
enc_val = enc_val << 2;
enc_val = enc_val | ((PIND & 0b1100) >> 2);
enc_count = enc_count + lookup_table[enc_val & 0b1111];
}
So, originally I had the two processes tested separately (vial position + encoder, then temperature regulation) and everything did exactly as it was supposed to. Now, I fused the code together and stored the vial position entry in the serialEvent() method to keep the temperature reading continuous and the vial position entry available for whenever I decided to provide input. However, when I put in a value, the program stops all together. I am able to see the number I entered (position: 5), but the Serial.println(enc_count) never gets printed. On top of the that, the temperature readings stop displaying readings.
Any thoughts? Need more information?