The Cole Protocol says that ships have to purge nav database when encountering an enemy. OK, that makes sense.
But in the case they win the battle, how do they find their way back to human controlled space?
Halo: Evolutions makes a reference to a "Cole Protocol return trip", basically after executing a series of random slipstream jumps, the ship is then allowed to travel to a known location (in this case, back to Reach base) in order to collect Navigational data to allow onward travel.
Find out what had happened on Algolis and make sure the weapons prototypes were completely eradicated. Then loop back on a complex and slow Cole Protocol return trip.
As to how this is possible, it's perhaps worth noting that the Cole Protocol relates to navigational data relating to Earth and the inner colonial planets. Presumably a small amount of Nav data can be held by the ship's crew that would allow them to travel to a neutral location or an armed Earth base.
All UNSC and civilian ships which come in contact with alien assets must have NAV computer/AI erased—destroyed if necessary—to prevent capture of core world locations.
Alternatively, they may simply be relying on the good old point'n'shoot approach, with ships heading toward known galactic structures until they get back to Earth-controlled space.