The intention over here is, to keep only respective collectorlist files of profiles.
Let me explain the dilemma,
We have 2 applications hosted on one server.
Separate profiles is created for another application by copying the working directory of default agent directory. Hence conf folders for new work directory is having same collectorlist files like,
collectorlist.AppTier1, collectorlist.AppTier2, collectorlist.App1WebTier, collectorlist.App2WebTier.
That is why I'm thinking to delete the unnecessary ones like collectorlist.AppTier1, collectorlist.App1WebTier.
Please advise on the same.
if the file isn't there, the agent will store a new one anyway.
It sounds like you are implying that you want an agent directory for each application? If all the agents are on the same host and there is usually only one agent directory (wherever the agent binaries where installed). It has nothing to do with profiles.
That's why collectors can get agent traffic from multiple profiles so a single group can service all your agents.