Hi Georgia,
A commonly used approach is to use all replicates that provide parameter estimates regardless of the successful minimization.
Other use more stringent criteria.
You can read the raw results file from the bootstrap. It is a csv file with each row having the parameter values of each replicate.
Typically we are interested in the 95 % CI of parameters which is computed by keeping the 2.5 and 97.5 % percentiles.
You can develop your own workflow starting from all replicate results, work out some exclusion criteria then compute your 95 % CI.
Please refer to the meanings of return codes for more details on what is a successful run.
A return code = 1 indicate no issues.