Salut,
an easy solution to this problem - keep two pre-edited app_info.xml files around.
What I mean - the file called "app_info.xml" tells BOINC which application to load. To use an optimized app, you need this file.
This file looks something like the following:
<app_info>
<app>
<name>setiathome_enhanced</name>
</app>
<file_info>
<name>SaH_5.15_KWSN_SSE3_Ben-Joe_2.0_B.exe</name>
<executable/>
</file_info>
<app_version>
<app_name>setiathome_enhanced</app_name>
<version_num>512</version_num>
<file_ref>
<file_name>SaH_5.15_KWSN_SSE3_Ben-Joe_2.0_B.exe</file_name>
<main_program/>
</file_ref>
</app_version>
[...]
</app_info>
I've coloured the interesting parts red for you. Wherever it says something.exe, you need to replace that with the name of the stock app, so it looks similar to the following (of course, you have to change ALL occurrences, easiest is to do "edit/replace/replace all").
<app_info>
<app>
<name>setiathome_enhanced</name>
</app>
<file_info>
<name>setiathome_5.15_windows_intelx86.exe.exe</name>
<executable/>
</file_info>
<app_version>
<app_name>setiathome_enhanced</app_name>
<version_num>512</version_num>
<file_ref>
<file_name>setiathome_5.15_windows_intelx86.exe</file_name>
<main_program/>
</file_ref>
</app_version>
[...]
</app_info>
Then save that file under say, app_info.xml.stock.
When you want to switch, stop BOINC. Rename app_info.xml to app_info.xml.optimized, renamed app_info.xml.stock to app_info.xml, start BOINC. It should happily resume crunching with the stock app.
Going back works exactly the same, just use the .optimized app_info.xml again.
HTH,
Simon.