When you recompile a new SPFx solution, it will generate by default new names for bundled JS files. This means that your existing instances are pointing to older versions of the assembly.
Steps would be as follows
- Deploy first version to SPO - sppkg package to app catalog and host JS files from some CDN location
- Perform modifications in the Solution using your editor
- This will generate new name for JS files - technically you could use same JS file names, but that not currently (end of May 2017) supported natively by the packaging tooling
- Copy new JS files to your CDN location - these are now new files
- Upload new version fo sppkg package to app catalog
- Perform an update in the sites for the package files, whcih have been deployed
We are looking into simplifying this in the future in SPFx tooling with few different options. This is however the current situation.