I made test on other versions and sometimes not working on simple cube.
version: 2.91.2, branch: master, commit date: 2021-01-19 16:15, hash: rB5be9ef417703
version: 2.93.0, branch: master, commit date: 2021-06-02 11:21, hash: rB84da05a8b806
version: 3.0.0 Alpha, branch: master, commit date: 2021-06-07 22:19, hash: rBef5a362a5b24

Don't know the reason for this.
On source blender B1 exist info about copy objects, but pasting doing nothig on target B2. When on target B2 doing copy to other this same situation, but inside B2 in B2 ctr+c/v working normaly. Then when trying paste from B1 to B2 have object from B2 that was in clipborard from last operation not from B1.

I'll be observing this. Have case where taking objects to old version blender due import sketchup and add-on not working on new, and other. Soo.. I'm working on 3 versions sametimes :]
Maybe is related with this https://developer.blender.org/T89270#1179302 ?

@ManBlender (ManBlender) So the issue is not between 2.92 and 2.93 but 2.91.2 and 2.93?

For all versions in any combination can meet this issue. If blender is not this same version then can't coppy, but if have this same instance of blender then copy procedure working normaly.

I'm not having any problems copying a plain Cube between 2.8, 2.93, and the latest 3.0 debug build on Windows 10.

Do you have all copies of Blender installed from the same place? I'm not aware of applications having their clipboards messed with when from places like the Microsoft Store, but I suppose it could be relevant.

Do you have all copies of Blender installed from the same place?

I using this same blender as other instances too.. but have 2 folders with this same version of blenders.

@ManBlender (ManBlender) Since we were unable to reproduce the problem, could you please provide:

• a simple project file that fails to copy between versions
• a precise description from what you are copying
• from what version to what other version you're copying

I meeting this issue more often, but seeing some possible related problem/case. For this must prepare special project and test this individually with confirmation.
But I can give words what problems is.

When I made duplication for object that are in some collection, then I distributed this object between other collection. In next step I parented the objects to other, that is in other collection.
Let we see this like home collection where is collection doors with doors_object_1, 2, etc/, this same window and this all in collection LVL1, then after duplication move this by outliner to created collection LVL2 and created Floor1 and Floor2 etc.. and parented LVL1 objects from this collections to Floor1 object to move whole. This all for move after extended shift+g (to select with children) and duplicate in next steps.
When I doing the shift objects as doors with doors_object_1, 2, etc/, this same window between Floor1 and Floor2 etc.. then in outliner object as children often don't have typical options around icons hide/show - I described different example that exist on image with intention.
On image and project file we see result of this type operations between collections and parenting.
I think the most often what I meeting is the situation where I can't copy the Cube.005 and Cube.006 - but on this file can't reproduce now this issue. On this file can't do ctr+z/ctr+shift+z on Object mode (sometimes when pushing ctr+z all objects diasapear - just one cube like starting project, but I made many steps/operation [this case is often with situation when can't copy - and doing this when see some strange cases around blender as risk to crash or situation when can't turn back some steps = soo.. some of objects as ready trying copy to other blender instance to protect work and include in other file after save] - some times I meet that whole GUI was black, and impossible to save, etc. and crash..). The case with undo I discover after I reported this issue - maybe have some sense for this.
Hope that is not here some issue as limitation or intended. Sorry again if something is not clear, I not understanding in precision the steps to reproduce events that doing problem. But maybe can help this view.

Also adding files around undo operations. And movie for this https://recordit.co/9a4IE05yGF

Do these Blender versions have different "Temporary Files" path?
If so, it is a duplicate of T82243: Impossible to copy/paste data between different Blender instances that are using different temp directories.

No, it's default as //

In T89288#1204977, @Philipp Oeser (lichtwerk) wrote:

then in outliner object as children often don't have typical options around icons hide/show

This means this object is a child of a parent that is part of this collection (the object itself is not in this collection though).
Not having corresponding hide/show icons is expected behavior in this case.

I'm not sure about this that working correctly due the example on video (looks like broken relation between edit in other objects - looks like relation loosed, but when edit in other object then edit show relation), this giving some intuition like object is "Free" from relation and disappeared from array of objects or something (in case exist).

Hm, if I read this correctly, we dont have a case that is reproducable yet

Look It's not file problem but operations..
Hmm.. Now I remember that on RCS experimented with "Extend".. and still have turn on function.. trying back to some new issues around this ctr+c/v problem and experience.. meet this same with bones. And before "Extend" meet this same.. so this can be maybe around "loosed relation" only suggestion)
https://blender.community/c/rightclickselect/P7PA/?sorting=hot#comment-48556

But wait.. it's sound similar like this, in case that on example I not used material.
https://developer.blender.org/T88504#1164769 - I recognized here the problem ctr+z for material, but maybe it's not? And when doing operations object can be broken do copy to other blender as not compatible?
Talking about coz often meet this when copied object with material, but ctr+z is often used, other users should report some crazy if exist..

Hard to help here

1. Main question here is: if I meet the alert when save fire "file written by newer blender binary expect loss of data" when working in 2 version of blender, eg. 2.93 and 3.0 also coping objects between can do for user problems eg. blocking copy?

2. Can be conflict from file /temp/copy_buffer.blend ? Maybe it's conflict around overwriting or windowsdefender? (I'm not using other antyvirus)

Maybe should add that I using BitLocker on discs, and C is not compressed and D, E disc are compressed.
https://developer.blender.org/T88724

// means 'relative to current .blend file', or 'relative to current directory (i.e. usually current blender executable directory)' if no file has been saved.

This is a duplicate of T82243: Impossible to copy/paste data between different Blender instances that are using different temp directories.