I would say that it is equally important your joins are occuring at zero-crossings. Even if the DAW appends files without any gap, you may still potentially hear the join (it will sound like a 'tick') if it's not at a zero-crossing and especially if it's a quiet/silent passage. Gapless does not necessarily equal seamless.
Reaper has auto-fading the beginning and ends of items as well as auto-crossfading enabled by defualt. This can get you what you want in a quick and dirty way by obscuring the join with the fades, but it doesn't always work. I'm not sure what other programs do, but depending on where your unintentional file division occured you could end up with a very audible edit point.
If you really are going for seamless joins this is how I do it in Reaper:
Go into the Preferences and turn off the default auto-fade / auto-crossfade.
Zoom way in. Put the cursor very near to the end of your first file, and tell it to Split at Zero Crossing (I think the shortcut may be Alt+Z, but check to be sure).
Do the same thing for the beginning of your second file. Yes this will shave a few samples off each file. They're being sacrificed for the greater good and are irrelevant unless you're doing a tempo-synced project.
Drag the two files next to each other in the same track (make sure Snapping is enabled on the toolbar).
Listen to the join carefully to verify you can't hear it.
At this point you can render out to a new file, but if you're going to split tracks at another point in your recording:
Select both files you are joining by Ctrl+clicking, then right-click one of them and select Glue Items.
Now wherever you decide to split later on, make sure you Split at Zero Crossing.