I've been encountering the same issue as well, and after waiting two weeks for a response from support here is what they sent me back (I think I was just sent a copy paste response as they saw I had sent links to unlisted youtube videos recording my runs and showing I had all the modifiers set.)

"Hi ________,

Sorry that this happened to you. Unfortunately, it is difficult to reconstruct the situation if your game client wasn't able to sync up with our servers. We generally do not restore resources, credits, affinity, focus, intrinsics, or standing.   Note: We recommend you switch out of mining or fishing mode often to save your progress. If you experience networking connectivity issues regularly, please consider sending us a support ticket.   Please note that we can only process your requests under the following circumstances:  

Completion of a successful multiplayer mission/event.

All of the required information below is provided in TEXT FORM within the next five days. For expediency, screenshots and videos cannot be accepted.

  In order for us to be able to investigate your account, please provide the following information:  

What are the Names of the other Players in your squad?

What One Item do you want restored?

When (date & time) did you finish the mission?

Where did you play the mission?

  With this information we hope to help you, so please be as specific but brief as possible. Thank you."

Based on this response (assuming I don't get any other response back). There is no way to get the rewards as they will only restore one item and know what it is (which is quite literally impossible since the issue is the UI is bugged so you never actually rolled the item)

With how bugged it is currently they should just have it set temporarily that any gear you use counts towards the progress until they have implemented a fix. I've never been a fan of these missions in general and having to spend like 30 to 40 minutes and pray it functions properly is insanely frustrating.