Hi Scott, here are my thoughts on your questions.
During a move operation, you can also choose between selecting components or bodies in the Move tool dialog window.
When you edit an existing sketch by actually going into it (i.e. will have Finish Sketch button appear in upper right) the timeline will automatically scrub back to the earlier position on the timeline where that sketch was made. Hence anything that was created after that sketch in the timeline will temporarily "not exist," which includes Snapshots in the timeline (which establish a new position/orientation for a component coordinate system, and body moves (indicated by 4 point arrow icon in timeline). Hence while doing in sketch editing, goes to a time before these component or body moves occurred, so will be in prior positions.
As to why timeline auto scrubs back when in-sketch editing (while can drag existing points around and change sketch dimensions in out-of-sketch editing without timeline autorolling back), is that while in in-sketch editing, projections from other geometry can be referenced to, and could potentially get a "time loop" if referenced to a geometry created after (the sketch currently being edited) yet also referenced to the current sketch. So needs to be this concept of linear time flow in the timeline.
For a workflow to prevent things jumping to prior positions upon editing a sketch in a timeline, here are some guidelines I try to follow (although if a model is imported from say Solidworks obviously can't follow this), that I recently posted in another thread:
1) Define a new sketch on existing geometry whenever parametric updating of position etc. is desired from changes of the existing geometry that defined to, and also to prevent stuff "jumping around" from edits in different timeline positions. But get in habit of first always creating and activating a new component, so that the sketch and subsequent body(s) will go into its respective component. This allows for among other things nice timeline condensing based on which component is activated, and also the sketches also moved by a component move. It really helps to turn on Inspect>Color Cycling for ease of component identification. Alternatively, uniquely naming the components helps with identification, even just front, front-right, etc. corresponding to view cube.
2) For duplicate parts, create copy(s) of the original component such that they are all linked (i.e. one changes they all change). The pasted component(s)'s positions can be defined to existing geometry via rigid joints. It is true that these subsequent pasted components will revert position or outright disappear when editing prior timeline features, but the original component will stay in place at least.
3) For performing fillets, shelling, etc. of the multiple components as one (or just reducing components as described below), they can indeed be combined first. If there are two or more paste linked components, it is important to choose these as tools for combining, with an unlinked component being the target, otherwise will get weird behavior (multiples of the combined component). The resulting combined body will go into the target component. The components now potentially left empty of bodies can be soft deleted if desired for browser simplification (although corresponding joints will disappear, they are still there/functional, and will reappear if corresponding component(s) brought back into browser via deleting the deletion event(s)
in the timeline). If need to modify a sketch of one of these soft deleted components, can simply scrub back timeline to before the deletion events. Allowing sketch relocations between components would be nice alternative. But a nice side benefit of this timeline scrubbing of deleted "body barren components" is that the scrubbing easily turns on or off visibility of all those sketches in different soft deleted components at once.
Besides merging components described above, you can drag a component into another component in the browser to make the former a subcomponent of the latter.
Selecting a component in the browser highlights blue the corresponding components in the work space. I also like using the component color differentiation mentioned above. This is especially good for multiple copy-pasted components that are linked -- they will all show up the same color. Also identified as being linked via having the same number after the the colon ":" in the browser, so to highlight all linked components could hold shift down and select in browser. As to breaking the link for one of these copy-pasted components, as far as I know, need to copy the component instance of interest, click on the very top level model component, right click and select Copy New, click ok if satisfied with current placement, then delete the other instance.
Jesse