Well, .cap files even from 0.8 in theory are still compatible, and we have a very good compatibility code that allows us to add, remove, or completely change sections of the file format as necessary, while still being able to load the old format. So we'll never change the format in a way that breaks all existing files.
Being beta sometimes we need to make changes in order to fix bugs which might affect - but not completely invalidate - older files. The physics bug deadeye was referring to actually only affected .cap files that were started with a couple of the more recent builds. The default world scales were incorrect, but the value was ignored. So I corrected the default value and fixed the bug that made it ignore the value - but this meant old files were now making use of the incorrect default value. The change was very simple (change two properties to 3.3% and it worked exactly like it did before). This was, like any other similar situation that has arisen or will arise, detailed in the changelog. If you keep up-to-date with the changelog, it's a trivial change. Very old applications in the newest version might suffer a few of these minor changes, and it becomes more difficult to track down all the tweaks after more builds get released.
The official line is that you shouldn't start any really serious projects in Construct until 1.0. This is true, but it becomes less of an issue the closer we get to 1.0, and large-scale applications are very good for testing Construct. You should back it up regularly however, including to separate media (this is just generally good practice with any software). Construct includes anti-corruption code - every time it saves or autosaves it verifies the data it generated is valid and can be successfully loaded. In theory, this means your .cap file is never corrupted (overwritten with data that cannot be loaded). However, there might be some other obscure as-yet unknown situation that causes an invalid file to be saved (even mature commercial applications sometimes do this). With regular backups, I'm fairly confident your work would be safe, but take precautions in case it is not.