A critical guideline to follow in liquid chromatography is to always inject your filtered sample in either the initial mobile phase or a slightly weaker solution. *Samples must be fully dissolved in solution before loading onto the head of the column. Injecting a sample dissolved in an immiscible solvent such as Hexane (vs ACN/ water) may lead to possible precipitation and analysis errors. Such a method would generally fail any validation.
Questions you need to ask:
Is your sample only soluble in normal phase solvents such as Hexane?
Would appreciate if you can elaborate on HPLC condition, particularly wavelength.
If you wish to analyse with RP HPLC only, then
Alternate 1 - Evaporation of hexane from extract and dissolve in ACN (if soluble) and make up with mobile phase.
Alternate 2- Add some 1,4 Dioxan (Spectroscopy grade- UV cutoff 215 nm) to dissolve the extract, and make up with ACN/Water system. If your working wavelength is >220 nm, it will not be an issue. 1,4 Dioxan, Tetra Hydrofuran (THF-UV cutoff 212 nm) & Acetone are solvents which are miscible with polar & apolar solvents. However, Acetone has UV cutoff of 330 nm, hence not at all useful.
While I agree with William's response in routine practice, I do know that you can get reasonable results using small injection volumes (5 µL or less) for non-compatible solvents on non-UPLC columns (e.g., 4.6 x 150 mm, 5 to 10 µm). We routinely analyzed a toluene based reaction by HPLC, and these results were very reproducible. These analyses should always start with a significant portion of organic solvent in the initial mobile phase (analysis of the toluene reaction above started at 50% MeOH since initial mixing tests showed taht all componenets had better solubility in MeOH vs ACN). However, you definitely run a risk of precipitation in the system.