Arduino with 2 echo sensors
In the 1 sensor program all the delays added together account for
62ms between samples.
In the 3 sensor program the sample code contains delays which likely
exceed 12ms (delays plus code execution).  So each sensor will not be
sampled faster than once every 36ms.
After you removed 1 sensor from the 3 sensor program, you increased
the sampling rate to about every 23ms.
It is likely a minimum amount of time is necessary between samples in
order for the HC-SR04 to recover.