Today I ran the latest version of the PnP PowerShell commands to apply some templates.
I noticed the following warning after I enabled debug
PowerShell_ISE.exe Warning: 0 : 2017-01-25 10:50:55.3041 [Files]  [Information] Skipping upload of file ‘Pages\default.aspx’ to ‘Pages’. 1497ms 7b0362d0-b49b-4d71-
Why is updating these pages not happening?
Looking at the code responsible for the warning
bool isNoScriptSite = web.IsNoScriptSite();
if (SkipFile(isNoScriptSite, file.Src, folderName))
// add log message
scope.LogWarning(CoreResources.Provisioning_ObjectHandlers_Files_SkipFileUpload, file.Src, folderName);
I just created a new tenant and I hadn’t enabled scripting yet.
If you don’t want to wait 24 hours then you can always attempt: