Using a register both in timer and main

I had a code like below to make some Flgas set/clear;

unsigned short FlagReg;

int main(void)
{
 ...
 FlagReg = FlagReg | 0x0001; // makes first bit TRUE
 ...
}

void Timer1Handler(void) _irq
{
  ...
  FlagReg = FlagReg & 0xFFFD; // makes second bit FALSE
  ...
}

This code seems to work. It works correct normally but it doesn't sometimes. It's because making second bit at timer1 interrupt doesn't work.

So, I thought of its assembly. It's like below:

main:
 LDR R0,[PC,#xxxx]
 LDR R0,[R0,#xxxx]
 ORR R0,R0,0x0001
 -> interrupt may occur at this line
 LDR R1,[PC,#xxxx]
 LDR R0,[R1,#xxxx]

If timer interrupt occurs at shown line what will happens? I think, makeing clear second bit will be not valid. Second bit was made clear and register was changed at timer0 interrupt but the value to write into register has been alerady calculated at previous line.

I hope that I could explain the problem. What can I do to solve this problem?

Best regards.