Before performing any solvent change, make sure the actual used solvent in the system is compatible with the new solvent. If the miscibility is not given, an additional flushing procedure with an appropriate solubilizer is necessary. Removal of the column from the system before flushing is recommended.
Example: if you want to flush your system from acetontrile:water to heptane, you need an additional flushing step inbetween with for example isopropanol.