After Skynet sent the T-800 back to 1984, the resistance defeated the machines soon after and took control of the time-travel machine. So when did Skynet even have the chance to send back the T-1000?
Immediately after it sent back the T-800, or as soon as possible as the technology allowed.
Time alteration was not understood by Skynet, so it had no idea what it would actually do if the timeline was altered so the logical course of action would be to send as many possible units with as many high priority missions as possible, which it does.
This would have been explained in a deleted scene in T2 where John and his men discuss and then use the Time Displacement Equipment (TDE). For plotting (and budgetary) reasons, this scene was removed although the time machine itself makes a reapparance in later films
The scene does appear in the novelisation though;
John struggled to recover, shaking his head. “Not yet. There’s one more thing we have to do.” He turned to Winn. “What’s your reading?” Winn glanced down at a palm-sized power meter dangling off his belt. Looked up at John with a puzzled expression. “Just like you said.” John took a deep breath, feeling the wheels of destiny grinding near. Then, mustering his courage, he abruptly strode out of the room. Winn started to follow. Fuentes frowned in confusion and hurried after, grabbing the tech’s arm. “What reading? What are you talking about?”
Winn indicated the meter. “This is the energy signal put out by the time displacement. I recorded two other identical pulses as we were fighting our way in here.”
Winn impatiently continued walking. Fuentes stayed with him. “What are you talking about?”
“The first must have been the Terminator going through to 1984.”
Fuentes was still confused. “Yeah?” Winn careened into the corridor and quickened his pace to catch up to his commander. Fuentes dogged the tech. “What was the second?”
“Another terminator, probably.” John’s footsteps clacked on the hard floor as he strode along the vaulted tunnel, followed by Fuentes and Winn.
Notably, this information wasn't shared with Kyle, hence his slightly conflicting statement that they blew the TDE as soon as he'd left. In fact they sent a T-800 back first, then destroyed it.