Multiple Ships
If the PCs have more than one starship, use the highest-tier ship’s tier as a base and add 1 to this value for each additional starship within at least 2 tiers of that starship. If none are within 2 tiers, add up the tiers of all the additional starships and add 1 to the base value if the total is equals or exceeds the base starship’s tier. Use this modified value when determining the encounter’s difficulty.
If there are multiple enemy starships, treat every pair of enemy starships of the same tier as a single starship of the pair’s tier + 2 (and every trio as a single starship of the trio’s tier + 3). If there are a number of ships of different tiers, use the formula for multiple PC ships to determine the final difficulty. For example, if the enemy consists of three tier 1 starships, a tier 4 starship, and a tier 7 starship, the final result would be a tier 8 challenge.
Source
Core Rulebook pg. 326