Thought I'd put a final update into this as the working solution.
After getting a couple of Cisco ASA 5506 units on site and creating exact copies of the IPSEC VPNs that I was having issues with, and running these test VPNs over other IP addresses on our twin internet links back to the firewall, I couldn't get the damn things to fail like the original links. They worked for a good couple of weeks without a dropped packet, even although I'd put the phase 1&2 settings to rekey every hour and half hour respectively in the hopes of generating enough debug traffic on both sides to see where the issue lay.
Went back to the outside agency in question, presented them with my findings, to be told point blank again, that the fault was on our side. After a pretty gritted teeth conversation with their network admin, he let slip that their configuration had a data transfer limit on both VPNs, where it would rekey every 4Gb of traffic. This was the first I'd heard about it, the agreed VPN documentation didn't have this noted, and PfSense IPSEC configs didn't have this in there (I don't think the StrongSWAN version currently in use on PfSense has this as an option anyway). After insisting that this be removed, both VPNs haven't failed since.
Cheers,
Monty