We had the same issue with some of our customer jobs being made into projects during conversion. It is an absolute disaster and completely unacceptable.  We use job type and class filters to combine multiple subjobs into a program report for tracking specific programs that cross multiple donors and regions.  It worked beautifully in desktop and now it is a wreck with some subjobs under the same customer moving to project and others staying as customers subjobs.  Furthermore, we track every single expense in Bill.com and Concur to a customer subjob and moving to projects for some subjobs is forcing us to have 3 data entry fields in Bill.com instead of the 2 we used before, which is causing issues for my staff.