Yep you have to log everything if you're going to use tracking as a weight loss weapon. Also i tend to discount the additional calorie allowance that exercise gives you on apps like MyFitnessPal - if I swim and run on the same day this can be 1000-1200 calories it suggests I've burned (which I don't believe), and it automatically adds it to your calories left in that day. I won't use that allowance except for maybe 100-200 cals of extra protein.
You have an ideal opportunity next week to kick start your next spurt of fitness and weight loss. Your body gets used to a level of intensity and in some cases starts to try to protect itself by not letting go of fat and using cortisol to wear you down (this also slows muscle protein absorption and directs fat storage around your organs). Having a lay off allows you to reset and go again. It also means you can ramp up the intensity a bit more which will help with fat metabolism.
Basically this is a great time to start doing HIIT / tabata, or incorporating KB swings into your press up/ pull up circuit. Refer to the circuits I suggested further back up the thread - start with a 15 minute session and build up to 30 mins. These will add functional strength, be low impact and complement rather than interfere with your cycling. Give yourself a target of 6 weeks to do this as a cycle and measure your results at the end. I'd do it 3 times a week for the first 3 weeks and 4 times for the second 3 weeks.
If you're not leaner and stronger after this I'll eat my hat!