Beatnik, losing muscle is a common concern when it comes to doing FS cardio. And the potential for muscle loss is there, especially if it’s done at higher intensity levels.
As you said, after an overnight fast glycogen, blood glucose and insulin levels are all low, an optimal environment for burning fat. On the other hand, it is potentially an optimal environment for burning muscle because carbohydrate fuel sources are low (to non-existent) and cortisol levels are high. But there are ways to minimize/prevent muscle loss.
As long as you don’t overdo it, you don’t need to worry too much about losing muscle. It’s a fact that muscle proteins are broken down and used for energy during cardio. But you are constantly breaking down and re-building muscle tissue anyway. Protein turnover is a daily fact of life. The goal is to tip the scales slightly in favor of increasing the anabolic side of things and reducing the catabolic side just enough so you stay anabolic, which results in your gaining or at least maintaining muscle.
How do you do that? First, limit FS cardio sessions to 30-45 minutes in length. Kept to 30-45 minutes, it is highly unlikely that amino acids will be burned as fuel. Additionally, the caffeine found in a strong cup of coffee will help mobilize fatty acids, resulting in the body burning more fat and less glycogen. If you can spare glycogen, you’ll ultimately spare protein too. An alternative to coffee would be an ECA stack.
Second, as Chris Merrow said, keep the intensity down to 60-75% of your MHR. Save higher intensity cardio for HIIT, which should never be done FS.
Third, make sure you have your diet dialed in. Too extreme a caloric deficit plus too much cardio is a formula for disaster, one that results in loss of LBM.
Losing muscle probably has more to do with inadequate nutrition than with excessive cardio. Adequate meal frequency, sufficient protein, carbs and total calories all stack the deck in your favor, making it less likely that there will be a net loss of muscle tissue over any given 24-hour period.
Fourth and finally, keep training with heavy weights, even while cutting.
There are benefits to longer-duration, low- to moderate-intesity FS cardio and HIIT, both. Optimally, you would be doing some of both. If you prefer to have a protein shake before doing your cardio, you could then do HIIT if you were so inclined.