Hi Empowersbane,
Returning to the question posed...I have a question. Do you mean an HPLC flush with the column in place or without the column?
In the case without the column in place (of course, the column will be flushed and stored as per the column manufacturer's recommendations in the perfect lab), why is MeOH preferred for flushing the instrument? Here are my two cents worth:
1. Methanol is less expensive than acetonitrile, isopropanol, or THF.
1a. MeOH is chemically stable, unlike THF.
1b. MeOH is miscible with the solvents used in RP chromatography. Buffers are generally more soluble in MeOH than in either THF or ACN...that said, the buffers (if used in the prior work done on the instrument) would have been flushed out of the column/HPLC prior to flushing the instrument only with a union connector in place.
2. Neat (100%) methanol is more viscous than acetonitrile or THF. Sometimes more viscosity works better for cleaning...neat IPA is more viscous than neat methanol, generally, IPA is also regarded as being a good HPLC flush solvent (at least by Waters and Agilent--the latest I've read is that IPA is now the "Gold Standard" for instrument-only flushing prior to more extreme cleaning).
3. Here's a link worth skimming over:
http://www.chromatographyonline.com/che ... etonitrileIn the case of acetonitrile, CRUD builds upon the check valve seats causing them to stick over time (I don't think much has changed in ACN manufacturing since 2008). Why flush and leave the HPLC instrument in a solvent which is eventually inimical to the check valves? To my knowledge, no such complaints have been spoken of regarding methanol and check valve function.
Please see what you think, and thank you!