I have many working projects where the schematic and PCB match. However if I clone the project and then without changing anything in the clone use Design -> Update PCB EasyEDA tries to remove about half the components and replace them with identical components. Even worse it sometimes places components in the wrong place, for example I saw an R9 placed where R19 was supposed to be.
Ok did that. There's no newgId in the Schematic, but one in the PCB file which I changed to false.
However also had several component labels move position and change to locked. Fixed them all now but why is this happening ? EasyEDA used to be a stable platform and I have loads of old designs that sometimes need support.
AND I've just edited the schematic slightly and it wants to change 3 unrelated components. I've checked the JSON and it's changed newgId back to true.
How do I keep it from not corrupting the file ?
Brand new interactions and interfaces. 
Easy to use and quick to get started. 
Hi
Your schematic prefix must didn't math PCB prefix as before.
for the old design, the editor will re-assign the component ID, to make sure schematic match PCB, it depends on component prefix.
this change since v6.3.39 https://easyeda.com/page/update-record-v6.3 for solve the component will be removed issue completely. for the new project, you will find that, this issue will not happen again.
How to fix:
1, make sure the schematic all components' prefixes match PCB component prefixes, and all prefixes are unique in the schematic or PCB.
2, open schematic and PCB file source, via: Top menu - File - EasyEDA file source.
3, find out all newgId, and set them as `false`. PCB do this action too.
4, Click the Apply button, the editor will re-assign the component ID base on the prefix.
5, Then schematic and PCB components ID will be matched, and will not remove the parts.
Thanks