Pega is not able to detect file upload dialog sometimes while doing multiple times same process of uploading/saving file. it stops refreshing adapter/browser elements and doesn't hook newly created window handle after continuously working after 20-30 cases. it works again if do the same steps again after failed case.
@chirag8838 It sounds like you may have a timing issue (i.e. you are doing something too fast). One thing I would look into is whether or not your control is getting created/destroyed with each iteration. You can see this in your RuntimeLogs. I would start there to first ensure that your control is getting created/destroyed after each automation action that would cause it (i.e. when you click the Upload button on your page it should get created, when you click the Open button on the dialog, it should get destroyed). Once you confirm that or identify where the issue lies, then you can start looking at what may have lead to that.