SQLite3.exe, etc. problems

[kinook]

UR DBs are SQLite3 DB's, but with .urd suffix, instead of .db / .db3 suffix, and with their special UR signature, i.e. first 15 bytes of the DB being _Ultra Recall DB_ instead of _SQLite format 3_

That is correct.

UR is able to open somefile.urd, even with the generic _SQLite format 3_ signature

Also correct. And UR can open UR format files (with either signature) if they have another extension (i.e., .db, .db3) or no extension.

but then again, stores this file with its own signature.

Incorrect. UR accepts either signature, and it does not update the signature of an existing file. So after you change a file (once) to the standard SQLite format 3 signature, you can open/edit it in UR and other SQLite tools from there on out.