If they're continuing to dish out PCNs, you'd be wise to do a bit of digging with the landlord/whoever owns the building and property to find out exactly what's gone on to result in them now operating on the site, and to see if the landowner can intervene.
A court claim is likely to eventually arise, and whilst you might have the makings of a good defence, it would in my view still be sensible to take steps to limit the value of the eventual claim, as there's never a 100% guarantee of success. Far better to defend a claim of £300 than £3,000.
Finally, I would ensure you have and retain copies of any evidence that shows that the space your car was parked in is allocated to you in your lease (Any maps for example outlining the boundaries of the space(s), or anything else that demonstrates that space is yours to use, etc.)
Re your questions, you can only appeal a charge to POPLA once that specific charge has been appealed and rejected by the operator.
Re BPA complaint, yes by all means, but again they will first expect you to complain to the operator.