OK Here is the response I received today, probably the same one the resto of you got but thought I would post it anyway. Haven't tried it myself yet but here it is, if anyone tries this before I get a chance to, let us know how it goes:
You can try excluding the files from being removed by the System Mechanic tools. This is one example of how to set exclusions:
1. Open System Mechanic by double-clicking on its desktop icon.
2. From the main navigation panel select Toolbox-> Individual Tools to display a list of tool categories.
3. From the category list select Clean Up System Clutter, locate the Junk Files Finder tool, then select the corresponding Start button.
4. Under Advanced, select the Custom Cleanup option.
5. Click Next.
6. On the Types of Junk to Find window, change the default settings as desired.
7. Click Next.
8. On the Locations to Search window, select the drives to search and specific folders to search as desired.
9. Click Next.
10. On the Exclusions window under the Excluded Folders section, click New.
11. On the New Folder Location dialog box, click Browse.
12. Select the folder you wish to exclude and click OK.
13. Select the Include Subfolders check box.
14. Click OK.
15. Click Next.
16. On the Safety Considerations window, select the desired options under the Additional Options section.
A. Ignore files that have been used within the last [ ] days
This option skips files that were accessed recently and provides a method of finding and removing files that have not been used in a specific time frame.
B. Ignore read-only and system files
Read-only or system file attributes usually designate important and necessary files that can be harmful to your system to remove.
C. Ignore files currently being used by an associated application
Removing a file currently used by another application may most likely cause unexpected and/or hazardous results. Although System Mechanic automatically prevents removing in-use files, if an item matches the configured search criteria, this option prevents the item from being displayed and/or removed.
17. Click Next to start the tool.
18. When the search is complete, the Inspect and Remove Junk Files window displays items to remove.
19. Inspect the groups to see if any application-related file patterns or folders you wish to keep are set for removal.
20. To exclude an item, right-click the item and select Exclude filename from future searches, or select Exclude folder from future searches.
21. By excluding these items in the Custom Cleanup mode of the Junk File Removal Tool, you will prevent all other System Mechanic tools (including the Quick Clean and Deep Clean modes) from removing the files, folders, and file patterns you wish to keep.
22. Remove any items as needed.
23. Click Exit when finished.
Follow these instructions on the other tools such as the Registry Tuner. Excluding the necessary items from this tool WILL NOT exclude these items from the Power Tools such as PC TotalCare, ActiveCare functions or the 'Repair All' function and it would be best that you run the repairs through the individual toolbox.