Still get this message. Where is the problem?
If this is in 7.99, it was reported (and fixed!) three days ago.
I use version 7.00. Should I update?
Sorry i don’t know if that bug was in version 7 or not, and if it was, when one might expect to see a fix.
I would not recommend you update to 7.99 on the basis of this bug (make this update-to-7.99 decision separately on its own merits, with a startpoint of “no”)
I would recommend you update to the latest available 7.0 version (7.0.1?
7.0.2?), on general principles and good practice.
BTW it is possible that those DRC messages are legitimate and correct, and not caused by a bug. If you haven’t already determined thus, you could check by deleting one of the footprints, doing an “update PCB from schematic”, and seeing if the DRC error goes away. If the error is still there, this is the bug I was talking about. If this “fixes” that DRC error, then there isn’t a bug at play here and for some reason your.footprint really is different from the library copy (I most often see this when i turn off the display of a 3D model for a “DNP” part)
You can run 7.0.x and 7.99 beside each other. (And 7.99 has an Inspect > Diff Footprint with Library, which includes a basic graphical comparison as well.)
…but once you save your project with 7.99 you can’t take it back to 7.0 
What do you mean by 7.99? Is there a beta version? I see only 7.01 version on Mac…
The issue is getting messy. I don’t know what is happening right now 
The board is looking good, all footprints are assigned. Also the gerber files look good.
Look at these 3 screenshots - when I “update PCB from schematic” it wants to remove unused footprints!
Why? They are exactly the same assigned in schematic. After that KiCad moves some footprints outside the board… and I have to track them again… What’s wrong?
7.99 is the development version of what will become v8 sometime in early 2024. That’s where tasty new features get added for the next major version, like the visual symbol/footprint diff Jeff mentioned, but it’s also incompatible with the stable version: once you save your work in 7.99, you can’t go back to 7.0.x. You can also expect a higher bug rate and generally things in flux, especially early in the development cycle like we are right now.
I wouldn’t generally recommend it for most people unless you’re pretty tuned in to the comings and goings of kicad development.
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Where I can download it?
Below the 7.0.x downloads on whatever flavour OS you run.
Just a further warning: The 7.99 is a DEVELOPMENT programme. It is frequently full of bugs and is not really suitable for serious projects until its final few months, AND it is INCOMPATIBLE with 7.0.1.
In case some footprints do not match the schematic (changed or added to the layout) Kicad asks to remove them. They ca also be mounting holes not present in the schematic.
To avoid any footprint to be removed it can be set as “locked” in the footprints properties.
The message says the footprints do not match the one in the library. It is the fisrt time I see this message. I cannot understand why because it seems you are updating the layout with the footprints in that library. I guess you have compared the footprint in the layout with the footprint in the library several times before asking here.
Maybe you have changed the references of the footprints in the layout and Kicad complaints because you have RV1 and RV2 in the schematic and Clk1 and Clk2 in the layout and the box Relink footprints to schematic symbols based on their reference designators checked.
You may have broken links between symbols and footprints.
How to repair the links?
BlockquoteMaybe you have changed the references of the footprints in the layout and Kicad complaints because you have RV1 and RV2 in the schematic and Clk1 and Clk2 in the layout and the box Relink footprints to schematic symbols based on their reference designators checked.
Blockquote
It looks like they need to have the same “Reference” name. Then it seems to leave footprints as they are.
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