General pruning advice is to prune off anything that is dead, diseased or damaged, and avoid pruning anymore than a third of the total foliage to avoid plant stress.
To see if the branch you intend to remove is alive or dead, gently scrape back a small section of the "skin", if the tissue underneath is still green it's most likely still alive and can be kept.
As the passionfruit has not been well maintained, it will be a tricky job to approach, and some of the healthy part of the plant is likely to be damaged in the process.
Choose some of the strongest and healthiest branches, and focus on saving those, removing as much of the dead matter as possible. It might take a few goes until you have the desired shape and it might take a season or two for the plant to recover and flourish.