In the Node.js / tiddlywiki --server version individual tiddlers are simply individual files, no? I find this is one of the benefits of using the tiddlywiki --server version because then I can commit those changes to a git repository (my backup method of choice) and let normal file version control deal with saving backups, seeing diffs, restoring older versions, etc.
One of the motivations for me to switch from the single HTML / TiddlyFox
saved version to the Node.js --server version was that I started losing
almost whole HTML files on save. I did not prove, but blamed, overly
aggressive virus scanning software noticing that a browser was updating
the filesystem repeatedly; or some other external cause. I got tired of having to lose all updates I'd
made since I last backed up the HTML file. I have not regretted adjusting to the Node.js version once I admitted that my requirements exceeded Firefox and TiddlyFox.
First questions: What OS are you on? Version of Node.js and, of course, version of tiddlywiki? Any external software that might account for this? Any other browser plugins? Any TiddlyWiki plugins?
When you say "new Tiddlers get saved OK", how do you know that? Can you inspect the actual .tid files in the tiddlers folder and verify that all the expected contents actually gets out to disk?
If you can verify that they are saved in their entirety I would conclude that something about re-opening them is failing. I'd start by temporarily eliminating all of the TiddlyWiki plugins; then disabling any browser plugins. I'd do that, too, if the filesystem verification proved that the 'saved' tiddlers were not actually saved.
Assuming tiddlers are making it to disk, are you creating backups of changed tiddlers? Can you easily restore them?