Thank you so much for writing this challenging, intelligent, heartfelt story for me. Yours powers of description take the reader into the tale from the very first scene - the evocative details of the dust motes (pink, then yellow) and cracked beams of light - and from there I really felt for Filius every step of the way. This line in particular was wonderfully evocative:
It had surprised him, how little he was over anything at all.
The intermingling of 'past' and 'present' scenes worked very well, believably showing how this unlikely pair could have become friends, and then more. I loved the way that your Filius remained unruffled by Severus' sharp tongue, and often found a clever way to get the last word. This exchange was hilarious, and summed that up beautifully:
"Sometimes I wonder if our relationship is only about you discovering new and ever more effective ways to force my compliance via orgasm."
"I could always stop."
"But just think what it would do to the student population, if I were to be unusually grumpy tomorrow."
I really liked seeing Filius in his own environment; he comes across as a truly three-dimensional character here (unlike in canon) and I applaud you for that! I love the way he is decent and stoic and brave, but not beyond a believable touch of self-indulgence and pettiness. He stood at the table he'd shortened from its compromise height the day after Severus had fled the castle - that's a lovely touch!
Severus leaving a puzzle - and a difficult puzzle, at that - for Filius after his death seemed a very Snape-like thing to do. I hope he manages to figure out the answers eventually! :-)