Is it permissible to file a lawsuit seeking compensation for missing the Umrah due to the loss of a passport by the company?

If the company was negligent and caused you to miss the 'Umrah, you have the right to claim financial compensation covering actual expenses, such as the travel ticket and visa fees. As for non-pecuniary damage that does not involve financial loss, the stronger opinion is that it is not permissible to take financial compensation for it. You may pursue legal action against the company to obtain your rights, acting upon the words of Allah Almighty: "Then whoever commits aggression against you, aggress against him in like measure as he aggressed against you," and "And whoever defends himself after he has been wronged - for those, there is no way [of blame] against them." However, if you choose to pardon and forgive, that is better, as Allah Almighty says: "But whoever is patient and forgives, indeed that is of the matters [requiring] determination."