Bug in Zotero for LibreOffice
If you copy and paste a section from a document containing references and move that section to another part of the same document the links to Zotero are gone. The links [x] remain visible but are in white in colour (the working ones are in grey) and no longer update when the Zotero refresh button is clicked.
DISTRIB_ID=LinuxMint
DISTRIB_RELEASE=19.1
DISTRIB_CODENAME=tessa
DISTRIB_DESCRIPTION="Linux Mint 19.1 Tessa"
~ $ libreoffice --version
LibreOffice 6.1.4.2 edc26d7faf41e406360d34efe1e39fe03035f7b0
~ $ zotero --version
Zotero Zotero 5.0.60, Copyright (c) 2006-2018 Contributors
But as Adomas says, what you describe should not happen for a traditional document merge process: If you insert citations as you describe in two document and then copy document two into document one, that'll be completely fine. It just starts getting iffy if you regular use copy between documents, for example.