We normally build one-to-many templates and have a few clients running assets in the 1k+ range. In my experience, you can "trigger" the mass approval and it'll take a long time but I haven't seen it fail b/c of the wait or being interrupted. I've come to not trust the dialog box that warns you it'll take 40+ mins or whatever - seems like it's rarely that long and when it does/has acted up or frozen that a refresh will bring it back on track (either cancel the action or load the completed update). This makes me think it's more like "sending a command" to the system and that will try to process live in the browser over time but that once the command is sent it'll work in the background regardless of the duration of your browser session (like if you were to close the window and come back later).
To be fair, some instances have way too many processes running at any given time so it might be a good idea to look for some down time to push a big update like this - if you've got 1k+ assets, chances are pretty good there's a bunch of processes running in the background as well.
If this is something you're running into that seems like it just wont update, you could think about cloning your template and batching it with some kind of asset limit like 500 EM only and then cloning the template to start the next 500 assets. Makes a bit more work for some pieces but might help to work around a mass-approval issue.
To your point about it getting corrupt: I don't think this is something that'd corrupt your template code, but you could always copy the code and save it as an .html file for backup-sake. The big push here is in updating the assets, not the template, but I haven't ever seen any assets get corrupt as a result of an update to a template.
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