Help! I Synced an empty JAXX wallet over one that had funds in it
Without the 12 word phrase, there is no way to recover your coins. So you must do everything you can to try to recover those 12 words.

It sounds like your new phone created a new wallet upon startup, so the 12 word phrase will not be recoverable from there: you'll need to work with your old phone. 

If the old wallet file is still on your old phone, then its no problem. Just open up the settings, and copy the phrase from there.

If the old wallet file was overwritten on your old phone, then you'll want to explore options to 'revert to a previous state', if you have a cloud backup service enabled this may be possible. If no option exists like this, you could explore professional data recovery options, but these will likely be expensive. 

Best of luck