It may be technically possible to transport between 46C and ECC6, but it is advisable to employ a change freeze.
The main reason for this is that your test landscape now is significantly different from your productive system. It will be very hard to regression/integration test anything fully.
If you also changed from a unicode to a non-unicode system you should be particularly careful.
Custom programs may be reasonably safe to transport, but you have to measure the risk very carefully - particularly in business-critical processes.
Doing transports of SAP-Repairs or enhancements may have very unpredictable results (and may not even be allowed). It will really not be a good idea to transport any SAP objects, as the functionality is likely to have changed during the upgrade.
It may be necessary to create a second DEV/TEST landscape that is 46C in the interim, if you cannot afford a change freeze. However this will require dual maintenance, and can result in it's own set of issues.