Replying to my own message, in case anyone else has a similar problem later. I came up with the strategy I would apply, then used the "record macro" option. It came up with something that seems sound. I'm sure it could be improved, but it does what I need.

The strategy is to copy the selected lines in register s, do the necessary search & replace and "join lines" on the original text in the buffer, copy that to the clipboard to be used in another program, then paste the original text from register s back into the buffer. Here is the macro.

Registers.copy(textArea,'s');
SearchAndReplace.setSearchString("///");
SearchAndReplace.setReplaceString(" ");
SearchAndReplace.setBeanShellReplace(false);
SearchAndReplace.setIgnoreCase(false);
SearchAndReplace.setRegexp(false);
SearchAndReplace.replace(view);
textArea.joinLines();
Registers.copy(textArea,'$');
Registers.paste(textArea,'s',false);

ghoetker, it seems like the simplest way would be to do a search-and-replace, where the replaced text ends up on the clipboard instead of in the source document, but I'm not sure if this is possible. Does anyone else know if it is?

I have come up with a solution, though. It just requires a bit more work. Basically, it involves the use of a temporary file (buffer) where we can process the text before placing it on the clipboard (register).

// Copy selected text
Registers.copy(textArea, '$');

// Paste copied text in temp buffer
jEdit.newFile(view);
Buffer temp = editPane.getBuffer();
temp.beginCompoundEdit();
Registers.paste(textArea, '$', false);

// Search-and-replace to remove "///" and newlines
textArea.setCaretPosition(0);
SearchAndReplace.setSearchString("///\\n"); // double backslash because need to escape it for beanshell
SearchAndReplace.setReplaceString("");
SearchAndReplace.setAutoWrapAround(false);
SearchAndReplace.setReverseSearch(false);
SearchAndReplace.setIgnoreCase(false);
SearchAndReplace.setRegexp(true);
SearchAndReplace.setBeanShellReplace(false);
SearchAndReplace.setSearchFileSet(new CurrentBufferSet());
SearchAndReplace.replaceAll(view);
temp.endCompoundEdit();

// Copy result to clipboard
textArea.selectAll();
Registers.copy(textArea, '$');

// Close temp buffer
temp.undo(textArea); // Undo so we don't get "File Not Saved" dialog.
jEdit.closeBuffer(view, temp);

Hopefully that does what you're looking for. If anyone has suggestions on how to simplify or improve this, I'd be interested to know, as I'm working on something similar.