I have seen the ways to modify an apk using apktools and adding android:debugging="true" but I have an apk that check for changes and crashes if any changes are made. Is it possible to capture the running thread and set a breakpoint using smalidea or something similar? I'm trying to capture some info from the apk in order to write something similar as I'm not getting any feedback from the original developer (in China).
You can't debug an apk on a user build of Android, unless the app has the android:debuggable="true" attribute in the manifest
However, if you have a phone you can flash, you can flash a version of Android that allows debugging of any app. userdebug builds allow this, for example. I believe it's the "ro.debuggable" system attribute that controls this.
Another option might be to try running the app in an emulator, which also allows debugging of any app.
Once you're able to debug the app, you can use smalidea or any other debugging tools that you want.