Annotation for hierarchical/multipage design that combine 3 ready boards designs in one (panelizing)

Layout
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I have hierarchical/multipage design. For now its 3 sheets with appended(downloaded) schematic/layout in each sheet. ( will be more)As it was all separate boards, it have own annotation. But now its all in one schematic.
How will it be handled that each of the 3 modules have a J1?How to handle that labeling?
Since each of the modules will be on a different sheet, can KiCAD automatically add a suffix? Example: J1-1 (for sheet 1), J1-2 (for sheet 2), etc?

I try to clear annotation and creat new annotation, but PCBNew dont want replace reference for components, for example: I have old J1 and new J8. Both on layout now, and I need to delete J1 manualy.
But its take long time to do it for whole board.
I not want to have to change all those manually. The opportunity for human error is too great. Becides I spent good quality time getting the components on each layout in just the right position, so now I need just connect together those 3 layouts.

Any advice?

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When annotating the schematic, you’ll see the annotation choice options.

“Start to sheet number *100…” will annotate J101, J201 in your example.

Be careful, it may change all your former references, i.e., R2 could be R105, etc.

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but it still dont change annotation on layout designs

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KiCAD isn’t able to support this kind of workflow yet - ie. designing a couple of boards separately and then joining them all together in one project.

I think there are 3rd party tools (scripts) there outside of KiCAD that help you a bit along the way, but not sure how good that works.

There also was/is a tool (or several) that can merge gerber files from different projects and create panels.
Ah, here we go… seems they made some progress from last time I checked.
It’s even open source!
http://blog.thisisnotrocketscience.nl/projects/pcb-panelizer/

If I did what you want to do I did choose one project (with the biggest/complicated layout) and copied/attached the schematics from the other projects to it and recreated the layouts of those boards.
Nowadays I’d definitely check the pcb-panelizer out, way less work (and errors) it seems and keeps your projects separated.

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It can change the layout too.
But I don’t know how have you created the layout and the netlist. Maybe timestamp doesn’t work because the way you appended the schematic and the layout independent designs but it should work.

Import the new netlist and pay attention to the options. Select the footprints by timestamp and delete extra footprints