I had lost Shadowmere for a long time too, probably for about 20 levels. I would occasionally run past, or fast travel to, the Dark Brotherhood Sanctuary in Falkreath many times but with no success. I would search the area nearby, because one time I found him battling a Frost-bite Spider near the bridge ambush west of Falkreath, and the place I thought he might have died up at Arcwind Point, using both Aura Whisper and good old fashioned legwork but this time to no avail. I was near to giving up any hope this time. My last resort was coming back here for possible strategies on finding him.
What finally worked for me was fast travelling to Winterhold, Riften, and Whiterun stables, then to Falkreath. When I walked to the Sanctuary there he was standing, right where the Penitus Oculatus agent should have been. I was completely unprepared to see him there after so long, but happy to see my old friend once again.
I have no solid evidence, but I think the travelling to the stables is what prompted the respawn at the Sanctuary. Maybe if someone has lost him they could try this out to see if they have success too.