How to seal swamp cooler wires going into roof
The best way would be a total do-over.  Penetrate the roof with conduit rather than liquidtight and use two boots for two pipes.  The conduit is optional - the boot will work better cinched to a conduit that doesn't flex or move than it will with liquidtight.  But using two boots really isn't optional.
If I really had to try to make it work as is I'd try filling the boot with expanding foam.
I'd remove as much of the debris as possible, and keep the two liquidtights at least a half inch apart.  Then I'd fill the boot a couple inches at a time, letting the foam set up each time.  I'd use the low-expansion type foam made for doors and windows.  I'd top it off with some roofing adhesive for UV protection.
But I'd only do that in a pinch, and I wouldn't be surprised if it leaked, you should do it the right way, use two boots.