Bad idea in so many ways.
Strange you don't seem too concerned about the emotional fallout side of things, but hey, that's your choice.
Mainly, what emmyloulou said - no "clause", many elements to being in a relationship, you'll be classed as being together, and people with mortgages leave a trail.
Financially and wrt benefits - good luck convincing DWP & CTX that you are still separated.
Local council wise - I'm going to (safely) assume you don't get housing benefit as it's jointly your house and he pays the mortgage. So therefore on him moving back you'd loose your single person's discount wrt council tax, and any council tax benefit would become means tested due to the change in your household circumstances.
Again, good luck convincing anyone official that you're separated once he moves back - your mortgage is still joint...
Councils are picky, but a) you'd only be looking at paying back council tax, so unlikely to be a large amount, and (more importantly) b) the council's fraud department would most likely need to get the DWP to investigate your claim for Income Support.
But it's the DWP & CTX you've gotta worry about.
And finally. As your mortgage is in joint names, your finances and credit histories are linked. Right now, those histories will show a divergence wherein he currently lives somewhere else. When he moves back, that will end.