It looks like you have indeed lost the links between the schematic symbols and the Footprints on the PCB.
Normally this is fixed with: Re-associate footprints by reference, but if you have re-annotated the schematic this may not work, depending on the settings during re-annotation. Did you re-annotate the whole schematic, or only add annotation to the new schematic symbols?
do you have a recent backup
seriously, updating reference designators IF not done carefully destroys hours/days of work. KiCad at least treats this a bit more intelligent than most eCAD software… (having a layout engineer rant at you for 5min because you “update” refdes when re-packaging a mentor project isn’t fun…)
What exact steps did you do? did you save the pcb file with these changes? if not close and don’t save. when you go to update from schematic there is an option to preserve ID
But Re-associate footprints by reference is not working here.
Yes I’ve re annotated the entire schematic.
What could be the options here?
But previously I’ve done these annotating entire schematic and then updating in PCB totally worked for me but for this time It’s completely messing.
I added new symbol and footprints to the connector, saved it and re annotated the entire schematic came back to PCB and updated the PCB from netlist but here footprints are moving while track remains in same position.
With these changes i’ve not yet saved the PCB I’m just trying to update and then closing without saving since it’s messing everything…
To preserve ID are you meaning to keep reference as is? It is not working…
when you click on “Update PCB from schematic”
do you have “relink footprint to schematic symbols based on their reference designator”
kicad typically using a UUID. doing this can resolve or make matters worse 
Read that “some error”.
I already explained what it means.
@Naib: Please do not confuse the subject with posting screenshots from V5.99 if OP is working with V5.1.x.
what can be done to fix
I also wrote that.
Again: Assign footprints to those 3 schematic symbols.
Yes you mentioned re-associating should work but here it’s not.
3rd and last time:
You have to assign footprint links to the schematic symbols to get rid of those three errors.
Those 3 errors have nothing to do with the annotation. That is a separate problem.
Please note that my question is not on those 3 errors I’m concerned with 4th error which makes the entire footprints position to move.
Those 3 schematic symbols are just block diagram used in block diagram sheet they do not contain anything it’s just a rectangular.
No it’s not.
The 4th error is just a general error that there are errors.
What happens if you turn on the checkbox for “warnings”, and “infos”. Those may give more information of what is happening.
Is it possible to share the files privately?
Sure you can.
You can zip your whole project, then click on my icon and send a private message.
Sure will do
Thank you
Lakshimi send me a PM, and I had a look at the project, did a **Eeschema / Tools / Update PCB from Schematic" with settings that seemed to give the best results and send those back.
It was enough to fix the assosciation between Footprint links in Eeschema and the Pcb.
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