My project is SUBFOLDERS but I think that doesn't matter. Anyway, the structure of subprojects is very simple:

• lib1
• lib2 (depends on lib1)
• app (depends on lib1 and lib2)

after starting the build (The project is qmake based) I see in console that all files is compiled without problem. But after compiling and linking step I see some strange error:

move liblib1.so ..\..\subdirs\output\
process_begin: CreateProcess(NULL, move liblib1.so "..\..\subdirs\output ", ...) failed.
make (e=2): The system cannot find the file specified.
make[1]: [..\..\subdirs\output\liblib1.so] Error 2 (ignored)

it looks that move failed to find a file. Note that building the same project for Desktop pass that successfully. 

The test project is in attachment. I used Android for x86 (GCC 4.9, Qt 5.11.1) for Android x86 kit

The only workaround I've found is to replace make with mingw32-make.exe from MinGW folder in project settings.