Based on your photos, it is possible that you have European fruit lecanium scale - a relatively common insect pest.

Soft body scale insects like these have many natural predators and it may be that no treatment will be required. However, if the population is excessive, your tree could experience some damage.

Here are a couple of links with more information about lecanium scale and how to manage them.
http://hyg.ipm.illinois.edu/article.php?id=804
https://extension.psu.edu/european-fruit-lecanium

It is unclear to me how the flies factor into the cherry tree problem.

You may find it helpful to get information and a possible treatment plan from a Certified Arborist. We suggest Certified Arborists because they must pass a test and must acquire continuing education. You can locate such individuals at http://www.treesaregood.org/findanarborist/findanarborist.aspx