Ideally, always uninstall the previous version of F# before installing a new one.
That said, I've done what you described (uninstall old version after installing new version, and re-install or repair new version) with success on my own box at home, so I think you should be fine there.
The VFSI implementation changed; it is no longer an "add-in" as of the new CTP version of F#, so it is safe to remove the add-in path altogether. VFSI is now implemented in a VS package instead, so no more need to deal with add-in paths.
If the VFSI window says 1.9.6.2 and the VS features (e.g. project templates) work, then you should be in a good state.
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I've got the 1.9.6.2 CTP release as ZIP, planning to use both for a VMWare-trapped Windows XP/VS 2008, and the enclosing Mac/Mono. Alas, clicking on alternative-install[-vs2008].bat or running them in cmd didn't change VS binding to a previous version I had (1.9.3.14). So I got the MSI and it did install CTP and also updated the version in VS. Then I realized I have 1.9.3.14 hanging around confusing things, and went to Add/Remove programs to uninstall it. Well, it took the VS binding to fsharpp altogether away, and left an empty group in Run Programs. So I had to rerun MSI to repair things.
As I'm staying away from MS as far as possible, and only F# and staying with my friends at Redmond enticed me back in for a peek, can you guys pls confirm that this endless writing over and registering/reregistering is safe, and leaves the system in a clear state? Basically, we need a set of .net components, some scary registry things somewhere, and VS bindings in place, all updated to a new F# release. How does one check it's all good and current?
Also, after uninstalling old F# and repairing new CTP one, when I push, outside of an F# file in VS, Alt-Return, I get a message that the Add-in command cannot be found, offering to remove it. When, however, I highlight a line of F# code and do Alt-Return, it happily executes. What gives?
Cheers,
Alexy