The answer can vary a bit depending on the software you have, but
try a text search/ replace Ctrl-F, or Ctrl-H. Or from the menu, Edit, Find/Replace or Text Search
Select properties radio button, Ref Designator or REFDES, etc...
If this doesn't work, because the ? is illegal, you need to change your properties file.
If using a central library, - Tools, Property Definition Editor
For "netlist flows" From the schematic
Look for REFDES or Ref Designator, Press the Advanced tab, edit the regular expression to add the ? like this (\u|\d|-|_|,|\?)*
Save and restart the schematic
If I understand the questions, firstly you want to reset all parts from being packaged with R1, R2, C1, C2 etc to unpackaged as R?, C?. Secondly you want to force packaging by sheet.
Neither of these options are available directly in the tools, once packaged you will have to manually reset the values and/or package by sheet. You can do this using the Add Properties command but it will take several iterations of manual intervention and is not an ideal solution. The built-in packaging process attempts to minimise part count and optimize the layout by grouping gates/parts together where it can which is why it might appear random.
With the next release of Designer we will provide an dd-in to mange reference designator assignment Add the ability to assign sequential reference designators refdes to components in a design using - D6577
BTW which flow are you using, PADS, PADS Professional or Xpedition - this question is in the wrong Community, it doesn't belong under PartQuest, once you let us know we will move it to a more appropriate site.