Sorry, this is a late reply, but we are also seeing similar issues of losing paths lately. I don't think we saw this before, but we are now seeing it (or we have been seeing this, but I didn't pay fully attention to notice it).
I am told by NetApp support to make sure clients (ESX/i, Linux/Windows) have Host Utilities (5.3 or 6.0 based on support compatibility matrix), and multipath configurations are fully correct. I will be going through my client systems to make sure clients are fully compliant, but have you tried host utilities with proper multipath config for ALUA? Does lun check_config -A show FC clients with partner paths used regularly?
If you have used host utilities, has it helped to handle well during fail-over/giveback?
I will report out what I find out on our next fail-over/giveback opportunity.