Don't worry about your deposit. Before you started the mixing process, ChipMixer gave you a session token. You can restore your session with this token. I hope you saved it. But the thing is, those session tokens are only valid for 7 days, and after that they expire. They can be extended, but you need access to the site to do that. Since these are extraordinary circumstances (the site being down), I am sure the support can help you here.

@ChipMixer
What happens with a user's deposit if the site doesn't come back online 7 days after the session expires, but he couldn't use the service or extend the session due to the downtime?   

it is difficult to determine whether these domains are really owned by the original Chipmixer.

Tor v3 link: http://chipmixorflykuxu56uxy7gf5o6ggig7xru7dnihc4fm4cxqsc63e6id.onion (chip mix or fly, new Segwit)
Tor v2 link: http://chipmixerwzxtzbw.onion/ (obsolete, non Segwit)
Clearnet link: https://chipmixer.com/