On Flores you will find few hotels of an international standard. Most of the 3 star and up hotels are in Labuan Bajo and surroundings.
Note that in Moni, Bajawa and Ruteng most hotels do not have aircon as this is not needed because of the altitude.
Comparing to Bali prices for accommodation are higher due to a higher standard (everything is more expensive) and also lack of competition. For around Rp 400.000 you will have a good sized and clean room, a good sleep, good bed, private bathroom (and aircon in coastal areas).
For the months July and August, Idul Fitri period and around Christmas/New Year it is wise to book ahead. Also, if you want a particular hotel it is wise to book as many hotels don't have many rooms. Book for a hotel which can be canceled without a fee.
Booking.com, Agoda.com and Traveloka.com offer the most choice. You also often can directly contact your hotel by email, WhatsApp or telephone.
Note that not all hotels can be booked via internet sites.
Try to get in touch once again. Emails are less frequently read than messages via handphone. Plus for some reason communication via email is less common in Indonesia. The problem also can be the local internet which is not as good as in western countries. If the problem still occurs please contact me.
Yes, except the months of July and August there is a good chance your choice still is available. Many hotels do not put all their rooms on the internetsites. So, just give it a try, or contact me if you need any help.