Hey.
You should remove the warning because it can appear even on regular q2 DM. Here's why:
your sv_ents.c function SV_BuildClientFrame
...
clent = client->edict;
if (!clent->client)
return; // not in game yet
...
for (e=1 ; e<ge->num_edicts ; e++)
{
ent = EDICT_NUM(e);
// ignore ents without visible models
if (ent->svflags & SVF_NOCLIENT)
continue;
// ignore ents without visible models unless they have an effect
if (!ent->s.modelindex && !ent->s.effects && !ent->s.sound
&& !ent->s.event)
continue;
if (!ent->inuse)
{
Com_Printf ("WARNING: Mod didn't nullify unused entity %d!\n", e);
}
...
When client connect to the server function ClientConnect is called. In the function you can see:
...
// they can connect
ent->client = game.clients + (ent - g_edicts - 1);
...
ent->svflags = 0; // make sure we start with known default
...
The client is initialized so the first "if" check in function SV_BuildClientFrame which I have pointed above is skipped. The second "if" check (if (ent->svflags & SVF_NOCLIENT)) is skipped also because "#define SVF_NOCLIEN 0x00000001" and the game sets it to 0. Now (when client is connected) he waits until his map is loaded and THEN comes function ClientBegin which sets "ent->inuse = true;". So there is a time when "ent->inuse == false", "ent->svflags == 0" and your warning is printed to the console

. Theoretically there is third "if" check (if (!ent->s.modelindex && !ent->s.effects && !ent->s.sound && !ent->s.event)), but when client disconnects game sets only ent->s.modelindex to 0. So the other s. things can be still != 0. I hope you get my point. Sorry for my english.
Thanks.
- Harven