There are two elements to your question and they need to be dealt with separately.
Ancestry changed your GEDCOM
And almost any other application package would have done so, too. Not always in the same way and sometimes you may not notice the change, but it will happen.
GEDCOM is now an aging standard and software developers have added their own extensions and enhancements. Moving a file from one package to another
leads to "approximations" and "compromises" as they push oval pegs into round holes.
The way to avoid difficulties is to select your preferred software (preferably on your own computer, not web-based) in which all changes are made in native file format and DO NOT EVER IMPORT
into that application. Create new sources, events and citations from scratch in that application to match your preferred methods.
When you want to use another application for a particular purpose, by all means export a GEDCOM but DO NOT BRING IT BACK. Any data file export should be regarded as disposable.
What should you do with the changes you made while on-line after importing the data? Open your main application and redo them there! And resolve not to be seduced by waggling green leaves again.
How should you use a Census record?
You should consistently apply a system that makes sense to you and to those with whom you plan to share.
For me, that means that I use a census return as a source of information concerning residence, occupation, education, religion, marital status and whatever else is available in particular jurisdictions
at a given point in time. I acknowledge that a census "has both a place and a date associated with it" but so does the publication of an edition of The Sydney Morning Herald newspaper from which I might obtain some of the same information about an ancestor.
For my purposes, the decennial census is no more an event in the life of my family than a triennial election. Of course I use the information recorded in the electoral roll; but unless 3xgreat grandfather was a candidate, the election was not an event to be recorded.
On the other hand, if you are part of a genealogical community that exchanges information on a regular basis, then you need to find their conventions and follow them. It is quite possible that you will find groups prepared to argue for each approach with equal fervour. The right way is the one that suits your needs.