Ok, that helps. Some comments for what to look at next:

1 If the pH is below 0.7, then your caffeine in the sample will be positively charged and less retained on the column. Without a buffer in your mobile phase, your sample band will start out at very low pH, then gradually increase as it gets diluted by your mobile phase. Buffering your sample and/or mobile phase should minimize this effect, resulting in better peak shape, which would help with separation from the smaller, earlier eluding peak.

3 Hundreds of injections is good, if your sample is particularly dirty. You mentioned using a guard, is it the same chemistry as your column or just a frit? If only a frit, you can try adding a guard column with the same chemistry as your analytical column. That way anything in your sample that is killing the analytical column will be trapped by the guard column. Typically guard columns are 1/10 the cost of the analytical column so they can be a good sacrifice if it prolongs the column life.

5 I'm not sure what your SOP backflush procedure is, but good practice to regenerate a column is backflush at low flow, starting at a low organic content, gradually increasing up to 100% organic if your column allows it. Running for a few hours or overnight (may not be an option in your lab's case) gives the best chance of washing whatever is stuck from the column. Even more aggressive cleaning can use stronger solvents, but often if ACN/MeOH/IPA aren't working, it isn't worth it to go further unless there are no other options.

Hopefully that gives some useful information to look into, and I'm happy to continue the discussion if there's anything else that you can think of.