The Opposite of Priority
Clearing the ECN field to zero within the network is very harmful to other traffic, and never useful.
Because ECN notifies congestion, it has the opposite effect to priority. So if you wipe ECN from certain traffic, you give an extreme advantage to that traffic versus others.
Explanation: The most common location of a bottleneck where packets are marked with Explicit Congestion Notification (ECN) is at the home gateway router into the Internet. If at some point further into the network, you clear the ECN field, the sender(s) will be blind to any bottleneck congestion. They will then send faster and faster until they overrun the bottleneck buffer, causing packet loss after adding a large amount of queuing delay.
Altho it's not pleasant, the senders of the packets you are mangling can cope with losing the benefit of ECN... However, it's everyone else that suffers. If some of the traffic passing through the same bottleneck goes off elsewhere in the Internet (rather than through the point where you're mangling), it will still see the extreme congestion notification as the buffer overruns (because you are not concealing it from everyone by your meddling). So the other traffic will rapidly cut its rate and starve.
Proper Solution
If a VPN tunnel egress is dropping packets with the ECN field set to 0x3, it will be because the ECN field on the inner IP header is 00. That's what a tunnel is meant to do, according to the ECN spec's [RFC3168]. The solution is not to blindly clear the ECN field on all packets (which will cause the above problems). The proper solution is to ensure ECN is not set to 0x3 on packets that started out with ECN == 0. Because that is an illegal transition according to the ECN spec (which is why the VPN egress drops them).
20th Century Dinosaurs
The 8-bit Type of Service field in the IP header (v4 & v6) was redefined in Dec 1998, and split into 6 bits for Differentiated Services, and 2 bits for Explicit Congestion Notification (ECN).
Only dinosaurs who are still living in the 20th century (resmon6 included), think that the ECN field is still something to do with prioritization.