Using nvim-jdtls conflicts with Eclipse

[ChrisAmelia]

I encounter an issue when I'm using nvim-jdtls and Eclipse at the same time,
the first for the language server and the last for mandatory company's tools regarding development.
The conflict happens, so far, with a Maven project especially regarding the target directory that is produced in the git repository.
Let's call this Maven project my-project.

More precisely, these are the steps I do

1. Run Neovim in my-project by opening a Java file: the language server is started, everything works fine.
2. Run Eclipse with the same project my-project, completions/diagnostics work fine for Neovim and Eclipse.
3. Update project with maven update.

The problem comes when running Tomcat. This is a hypothesis: the target directory is copied into Tomcat,
but is inconsistent due to the two above altering that directory.

What can be done to avoid this conflict?