There are low level workarounds, such as playing multiple audio tracks simultaneously.
If it were me, I would take a copy of the audio file, grab the last three seconds, cut and copy it to the front, then delete all but the first six seconds. Create a fade so that it stars and ends in silence and peaks at three seconds (use a "bell curve" envelope so that it smoothly fades in and out. Now grab that six second section and move it to the right in your audio editor so that you end up with a track that is precisely the same length as the original track. When you bring this patch track into Hype, set it to start three seconds after the original and to loop as well. This will cover the gap and stay in sync.
Note 1 - The above is based on the idea that the audio track is designed to loop seamlessly. if the start and end sections different (such as being at different volume levels, different content, or the rhythm is off) you would need to smooth this out or it will be noticeable.
Note 2 - You may have to play with the volume levels at the loop point so that the patch doesn't create a swell in volume.