I am not the greatest with Blender but here are some general tips I have picked up over the years.
This has happened to others because the have hidden or locked objects in the scene. You can reveal hidden objects by pressing ‘Alt + H’ and unlock objects by selecting them and pressing ‘Alt + G’ to clear their location.
If your character is in a group, pressing ‘Ctrl + Alt + G’ is used to remove objects from a group. If your character does happen to disappear, after using this shortcut, this I believe means that the character was part of a group, you can bring the character back by going to the outliner panel, expanding the group, and selecting the character object.
Those are some general tips I have heard before, however more screenshots like mentioned above can definitely help. I hope I am not misunderstanding this.
Also here is a list I found online that might help with your error message:
The error message “Nothing to remove, Manifold edges not found” typically occurs when you try to perform an operation that requires selecting or removing manifold edges, but there are none present in the current selection.
To resolve this error, you can try the following steps:
Make sure you are in Edit Mode: Switch to Edit Mode by pressing the Tab key or selecting it from the mode selector at the top of the viewport. This ensures that you can perform editing operations on the mesh.
Check your selection: Ensure that you have selected the appropriate geometry (faces or edges) before attempting the operation. Right-click on the desired faces or edges to select them. You should see them highlighted.
Verify that the geometry is manifold: Manifold geometry refers to a continuous and watertight mesh without any holes, isolated edges, or non-manifold elements. The operation you’re trying to perform requires manifold geometry to work correctly. Make sure that the selected portion of your character’s mesh is manifold. You can do this by inspecting the mesh for any disconnected or non-watertight areas and fixing them if necessary.
Try alternative methods: If the specific operation you’re attempting is giving you trouble, you can try achieving the same result using alternative methods. For example, instead of using the 3 key to switch to face mode, you can manually select the desired faces by right-clicking on them or using other selection tools in the toolbar.
Reset Blender preferences: If none of the above steps work, you can try resetting Blender’s preferences. Sometimes, unusual behavior can be caused by corrupt or conflicting settings. To do this, go to the Edit menu, select Preferences, navigate to the “Defaults” tab, and click on “Load Factory Settings.” Be aware that this will reset all your preferences, so make sure to save any custom settings or configurations you want to keep.