Sponsored License Expired

Hi,

My Company's sponsored license has expired, its a small firm and no body noticed the expiry date because my previous MD has retired and New MD does not come often, he has not changed the email address so all the information was sent to previous MD's email which we dont have any access.

License got expired in May 2018 but it came to notice when my colleague got curtailment letter last week.

We are 2 employees with tier 2 general visa.
My 5 years completes next year in 2019 and I would be eligible for applying ILR.

our company is ready to apply for a new license and ready to hire both of us again but the question is
will this effect my ILR application in June 2019?

I have already booked a ticket to India as i was not aware of all this issues . will that be ok for me to travel to India as I have not received any letter from home office.

Please do let me know it will be a great help.

Thanks