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.
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