All three of your issues are related to a single root cause. Unlike the CAD (computer aided design)
world, where data draws itself on the canvas (and copying a layer makes a clone of the previous data),
in the GIS world, data is something that is manipulated or drawn. This makes for two separate sets of
resources, Data and Rules.
The ArcMap drawing document (.mxd) is the rulebase by which data (.shp,.gdb,.sde,...) is represented.
In order to modify file geodatabase data, while preserving the previous version, you must make an
explicit copy of the data (Export, or any of dozens of other ways), make the copy the active edit layer,
and edit that. Anything else may corrupt your original data.
The nice part of the GIS model is that data doesn't get trapped in documents. It can be shared by
different applications for different purposes, and different renderers can be applied to make the
same data available to different purposes, without making dozens of copies of the same features
(which would then need to be reconciled when edits are necesary).
Of course, because the rules are partitioned from the data, you can quickly get yourself in trouble
if you fail to move the data at the same time you move the rules (this is one of the reasons why
enterprise geodatabases are popular -- they provide a single repository, accessible by the entire
organization for data resources). There are tools (Properties... Source) to re-associate layers with
data which is no longer at the previous path, so keep an out for exclamation points in layers
which no longer render.
Once you internalize this difference between CAD and GIS, you'll never experience these sorts
of issues again.
- V