Try lower pKa acids, formic or TFA at lower ratio. This way there will be less evaporation, especially at lower working temperatures. Alternatively, use low binging glassware.

You can use up to 100% water on silica gel so long as the mobile phase is neutral or acidic. Silica dissolves in polar, basic, mobile phases. See: https://www.teledyneisco.com/en-us/liquidChromatography/Chromatography%20Documents/Application%20Notes/RediSep%20Rf%20Gold%20Silica%20and%20Highly%20Polar%20Solvents%20App%20Note.pdf

Try using less acetic acid in case the compound is basic. The acid might be ionizing the compound, making it very polar. Reducing the acid might allow it to elute, perhaps as a broad peak.

How did you get to this step? What extraction steps before your column? That would give some clues to the compound and how to run it on a column.

This fraction now must contain some dissolved silica gel. I would suggest you to go through a short packed reverse column (C18 silica) to remove the silica gel. Then for dealing with this high polar fraction, you can try reverse phase column or LH-20 size exclusion column to proceed the next step.

I would suggest you can use sephadex column to purify the high polar compounds instead of normal silica column or else you can use preparative TLC method also.