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If I record in WAV, create an Audacity project that links to those files, modify the project, export the final cuts, save everything, convert the WAV files to FLAC to save space, then convert the FLAC back to WAV in the future and open the Audacity project again, will anything break?
Put more simply: Will going from WAV->FLAC->WAV result in bit-for-bit–identical WAV files before and after the conversions, or introduce errors that might mess up Audacity?
Since FLAC is the "free lossless audio codec" it should retain the same bit-for-bit audio data. This also implies that the audio parameters (bit rate, sample rate, channel count will be the same. What's not certain is if other meta-data in the .wav file (e.g. comments, cues, etc) will be preserved when converted to flac and back again. If you have none of this, then you should be fine. If you do need preservation of these type of data, then it would depend on the conversion tool you're using.
But certainly do test at least once before converting all your projects.
Another alternative is to avoid any need for conserving space and invest in an adequate archiving solution: either a large HDD or some optical solution such as CD, DVD or Blu-Ray (just depending on how big the total projects are). It's nice to have an archive of discs simply labeled with your project name on them and sorted by project date. I'd imagine that the time it takes to copy to/from this optical media would be comparable to the time it takes to convert to/from flac/wav.
