There is much to like about the Digitakt, but sample management is not one of them.
In my opinion Elektron severely dropped the ball on this one - in particular their inability or reluctance to produce a PC based sample management tool to compensate for its arcane and frankly ancient file management.
The problem is that once you reach a point where the 1Gb sample drive is full, it’s almost impossible to free up space, without destroying the links to the samples that you’ve previously used in a project - which in turn breaks your project. At this point, an option is to buy another Digitakt or go through all your projects - record them out as a performance and then wipe your DT and start again.
The only way I found to work around this daft limitation was to strictly restrict my project source sample pool to a specific and uniquely curated folder of samples. It’s not a particularly elegant solution - but at least its possible to archive off all the source samples for a project and thus securely back it up. But its frustrating because you cannot use the Sound Pool or grab a sample from another folder without running the risk of later breaking the project.
Sure Elk 3.0 helps with the archiving of a project but it can’t find and archive the samples and without the samples the Digitakt project on its own is worthless.
So make a fresh sample folder of fresh samples per project and force yourself to only use samples from it.
Also annoyingly if you have a favourite sample that you want to use in multiple projects - you really need to make it unique as far as the Digitakt’s file intelligence is concerned otherwise it will merely look at the sample - reference it to another that’s already on its drive and then you’re back to facing the problem of subsequently breaking your project.
So again, make a fresh sample folder of fresh samples per project and force yourself to only use samples from it.
Good luck!