The Finders functionality for folder merging is very limited.
It wil work if the folder being copied has no sub-folders.
If you wish to copy an entire folder structure from one place to another, you can use a Terminal command:
ditto -V sourcefolder destinationfolder
This will copy sourcefolder into destinationfolder, retaining the unique files of destinationfolder, but over-writing any files that have the same name as the one in sourcefolder.
Alternatively, you can use the a different command to prompt you as to whether or not you want to over-wrote files that have the same name:
cp -R -v -i sourcefolder/. destinationfolder
Thank you. This helped clarify. I am not comfortable with using language and / tools I don't understand, especially where the cost of getting it wrong is so high. Do you(or anyone) know of any tools that mimic Windows' functionality? I have come across utlities like DeltaWalker and Araxis and Big Mean Folder Machine but these seem rather OTT, and MoveAddict which seems to have limited funcionality and takes FOREVER to merge firing off the mac "ping" for every action it completes. Ifnot, will i be better to merge my folders using Windows and then copy the output back to mac?
Thank you again, I appreciate you taking the time to reply.
No problems - anytime!
The fact is that a GUI tool is not really any safer than the command line - it is just a different mechanism for executing a program.
If you feel more comfortable doing the merge in Windows, then it is probably a good idea to go with your gut! File operations such as this are one area where the OS X GUI is arguably behind Windows.
On the other hand, I actually feel more comfortable using the command line these days - it gives fantastic control and flexibility. Then again, I also like skydiving as a sport.....