HingeJoints stop working when the scene containing them is reparented

[tcoxon]

Godot version:
3.2.2, but also reproduced in upcoming 3.2.3, in commit 9bf5a0b on the 3.2 branch

OS/device including version:
Ubuntu Linux 16.04, 64-bit
GeForce GTX 970 with NVIDIA 384.130 driver
GLES3 backend
Bullet Physics

Issue description:
Removing a scene containing a HingeJoint from the tree and then re-adding it causes the HingeJoint to stop working.

Steps to reproduce:

1. Run the reproducer
2. Observe the brown beam at the back of the scene swinging in the XZ plane, on a hinge
3. Press space bar to remove the scene from the tree for a split second
4. Observe that the brown beam collapses and falls out of the plane. The hinge is no longer affecting it

Minimal reproduction project:
Physics-RemovedNodes.zip

The Reproducer scene contains a number of physics bodies:

1. A green CSGBox providing a static collision
2. A brown beam (a RigidBody on a HingeJoint) that is central to this issue
3. A white capsule (a KinematicBody) scripted to move back and forth, pushing the beam back on its hinge
4. The other elements of the scene are not relevant to this issue (they're for '_body_enter_tree: Condition "!E" is true' errors when a scene containing an Area is removed and re-added to the tree #41397)

When you press space, the scene is scripted to:

1. Pause the tree
2. Remove itself from the tree root
3. Wait 0.1 seconds (which may not be necessary?)
4. Then re-add itself to the root and unpause the tree

[akien-mga]

CC @madmiraal @AndreaCatania

[WilliamTambellini]

@akien-mga could you please flag that one for a 3.2 bug fix release ?

[akien-mga]

Any bugfix relevant for the 3.2 branch will be considered once there is a fix (the PR gets the cherrypick:3.2 label).

[madmiraal]

Related to #25689 and #31711