My allergic conjunctivitis has gone today, can I start using mascara again?

Suggestions. I would suggest using a brand that is hypoallergenic and cleaning the mascara wand with soap and water. If you know your allergic triggers such as pollen, then taking steps to avoid the triggers, will help prevent flare ups.
Probably. You need to be sure that your eye symptoms are from allergens other than your mascara, because cosmetics can cause allergic reactions as well. Assuming you've used this mascara in the past, and you know for sure that you're reacting to allergens in the environment, it is ok to use the mascara once the conjunctivitis symptoms (itchy, red, watery eyes) have gone away.