Target Heart Rate

I'm going to guess that when you say "target heart rate" you're referring to the so-called "fat burning zone"?

The fat burning zone is low intensity cardio (around 60 to 70% MaxHR) which does burn proportionately more calories from fat than carbs (glycogen stored in muscles and your liver). In terms of weight loss higher intensity cardio is more effective inasmuch as you are burning a much higher number of calories overall and your cardiovascular endurance improves considerably.

Lean muscle mass loss is only a concern if you're not eating enough protein, have a very low % of body fat and have a very high training volume (think marathon & ultra-marathon).

You mentioned that you're consuming "a ton of protein" (hyperbole I hope), if you really want to err on the side of caution include strength training in your fitness program (it's a good idea in any case)

My RHR is low (about 55) and I am 39 years old female. If I take the 226-39 to get max heart rate of 187

My heart rate is generally at about 150 which is a little above 80% max heart rate . Is that too high for someone who has a lower resting heart rate to start with?

Mine (according to this formula) is 226-41 = 185. That's probably somewhat close to accurate. I haven't gotten mine up over 182 when I'm running however it's not a big deal for me to have it sit at 175 for 30 minutes. That's hitting about 94% of max.

Am I going to lose muscle instead of fat at that rate? I can feel my muscles now that I could not feel before but I am afraid that if I continue at that rate, I might lose lean muscle mass too.

Just don't do intense cardio for hours at a time. Keep your cardio down to under an hour and you probably won't run into this issue. See my picture where I'm holding up a tree? That's from a couple weeks ago. I weigh 210 and don't have any issue holding on to muscle. Sure I could be bigger or bulkier if I did little to no cardio but doing a fair amount won't strip off your muscle. To me it's better to balance muscle and cardio fitness.

And I know I am losing too quickly (13 inches and 13 pounds in 3.5 weeks) but I also feel great and I eat a ton of protein.

You might need to up your calories. This morning I burned 983 calories on my run. Obviously I need to eat that back or it's going to catch up to me eventually and make me drop weight. It's all about calories burned vs. calories eaten. If you're dropping too fast then eat more. Personally I wouldn't try to drop more than a pound a week. Too much can risk muscle tissue loss.