Hiya Lauren
It could be redirected aggression. Sounds like it to me. I have the same with my two since the 1st stray kept coming in to their cat proofed garden and their relationship has not been the same close one since.
Sounds like the trigger was the outsider cat with Milo.
Well done for the trying the feliway
Has Milo or Louis started peeing indoors to out their scent down? Has Milo shown signs of "big Boss" Alpha male ie blocking the cat flap, blocking the litter tray, food trays?
Here's some info
-http://www.icatcare.org/advice-centre/cat-behaviour/aggression-between-catsWhy did my cat attack its companion when it saw a strange cat through the window?
Cases of re-directed aggression from one cat to another, triggered by an acute sense of threat from an external source, are also relatively common if there are underlying tensions. Cats have a very keen survival instinct that utilises an internal system referred to as the fight/flight mechanism that releases adrenaline, pumping the muscles full of blood, to prepare the body for danger. This massive emotional response can be triggered by a sudden sound or movement or the sight of another cat through a window but the ‘attack’ may be accidentally launched towards an innocent cat if they happen to be in the wrong place at the wrong time. Relationships between two cats in a household can be irretrievably damaged under these circumstances. Once again, the advice is to separate them into different rooms for 24-48 hours until they have both calmed down. If a re-introduction at that stage still results in active fighting it may be necessary to segregate them for a longer period and treat them like complete strangers meeting for the first time. (link to introducing a cat to a cat).
http://www.catbehaviorassociates.com/redirected-aggression-in-cats/Re-directed Aggression - This can manifest itself in several ways. For example, Your two cats usually get on just fine, but when one of them walks in one evening he sets about attacking your other cat to such an extent that you have to separate them (never use your hands - use a pillow or a cushion - you will be next to be attacked). Again you are left thinking - what was all that about? You have assumed that the conflict is between your two cats, when in fact the conflict happened outside. The big cat from next door was in the garden again and your cat had just had a fight with him - his senses were still in a heightened state when he got back inside the house and your other cat took the full force of his frustration - he just happened to be in the wrong place at the wrong time.
What to do: If you think your cat is enduring this kind or aggression then it is very important to establish the cause. You will need to keep a detailed diary of when they occur and how often. It may be that you have to keep your own two cats separate for a short while when one of them comes in, so he can calm down.
If it continues, you may need to keep them separate then slowly reintroduce them again.
If the cat from next door is coming in the cat flap or is staring through the patio doors, it may be an idea to cover the bottom half of the doors so he can’t see in or block the cat flap up. NEVER try to calm a cat down - this is only something he can do himself - you risk getting injured yourself if you intervene while the cat is still in a heightened state of anxiety. It may be that your own two cats need to be separated as seeing each other cat may just ‘trigger’ the aggression again, even though your other cat was never involved in the first place - a bit like us - we have a bad day at work and take it out on our partners when we get home - nothing to do with them, not their fault - but you take it out on them anyway!
