I had the same missing data issue and I was using jsPsych + Pavlovia + Prolific. One way that largely reduced cases of missing data for me is the solution in this post How to provide return link in jsPsych for participants recruited through prolific?. Basically, I suspect that the chance of the data being lost could be reduced by adding a delay after submitting data to Pavlovia and before redirecting to the Prolific completion URL. I was never able to recover the missing data though.