(PORTABLE version on Win7 Pro 64bit)
I've TRIED to replicate this, but the link to the created note remains visible (and active and functioning properly) throughout countless Refresh cycles and switching between DIFFERENT databases, and after fully closing and re-opening (any) doogiePIM database.
I created a new "critter-TEST-db-01" database, and as instructed, from the Homepage, a "critter-TEST-doNote-01". BOTH are located in "..\Data Files" on my HDD, and BOTH were successfully written to 'doogiePIMSettings.ini' (line 1132 and 2347) - then I switched between 3 different databases, did several "refresh" during each session (per [F5] and also clicking "Refresh" on the context menu - the ONLY thing that changed was the "Quote of the day") and also closed doogiePIM completely. The link to "critter-TEST-doNote-01" was ALWAYS visible within "recent doNote Documents", and despite more refresh than I cared to count, I could NOT replicate a "missing link", hence I think the problem might be LOCAL to critter's computer.
I hope this helps.