From an AMD standpoint overclocking the GPU will most likely lead to "hung WU" which means that most likely your video cards drivers crashed. I'm actually underclocking my R9 290X TRIX cards just to keep them stable and that is an ongoing experiment.
Overclocking will most likely result in a reduced PPD due to instability if you are using AMD GPU's. I can not say if it is the same for Nvidia.
I also use the FAH Control client. I have not been able to keep any of the R9 290X TRIX cards running at 1040-1300. I'm currently at 947-1000 on most rigs. One computer is at 937-1000. Another is at 917-1000 and still shaky. Every time I see a hung WU I reduce the core clock speed by 10 and reboot. If I get to 900 on core clock speed and I'm still getting hung WU's then I reduce the memory speed by 50 and start again. It is an iterative process but I did drop from 1250 memory speed straight down to 1000 initially after I ran into issues even after reducing the core clock speeds and then I started the process over again. If you are wondering where I got the 947 from it is an arbitrary number that another user posted so I restarted there.
Watch your logs for each GPU. If the logs shows a WU is 25% complete but the client shows a higher number such as 30% then that WU is hung and will not finish without intervention. If you let it go long enough it will eventually show as 99.99% complete in the client and just sit there. That is the indication that something happened and then you need to start bringing down your clock speeds to find what is stable. You do not need to wait for the client to show 99.99% before you act. In fact, if you do you will lose hours because work isn't really being done.
If you have not run into this issue and have been running for some time (days) your cards may be able to handle it. That has not been the case with any of my 15 R9 290X TRIX cards though so I would say the odds are against you.
Some tips: If I do in fact see a mismatch I reboot the machine without pausing folding in order to reset the WU. It may take a little while in order for the client to show movement again but the log should show it fairly quickly. Some have reported that you can pause folding and then start again but I always reboot because I have found the driver crashes often times make the system unstable. I prefer to start over.
To reiterate: Watch the logs. The client is not a reliable source of information. Frequently check the percent done in the log and compare it to what the client says. Don't trust the client display. That goes for PPD estimates as well. They are also very unreliable in the client.
If you do run into hung WU's it would probably save you a lot of time and effort to start where I'm at and if you run stable start adding 10 to your clock speeds if you want. I can say the overall PPD have not changed much even after all the downclocking. The biggest killer of PPD is hung WU. You want to avoid those at all costs.