Vinyl Liner Stain- want to close -- what to do?

Last week in Pa the leaves are falling and temps are dropping so activity is less as swimming is about over . Open today for 1st time is 4 days and lots of leaves on pool bottom and in skimmer basket . Cleaned everything only to find some discoloration or stain on liner . Mostly on tHe side where my one return line is . Check FC and it was about 1.4 and PH 7.4. I had a old Jacks Stain kit and applied Stain Pack 2 and 3 with maybe some less noticeable . I then checked chemicals FC 1.4 Alk 120 Hardness 160 PH 7.4 . Normally have been keeping FC at 3.0 Also CYA Like 30. I have shocked with liquid bleach . Also tried some ascorbic acid on it and no real impact .

Liner is about 3 years old and on former liner felt I had some staining coming from under the liner so we treated ground before we put this liner in .

Want to close on Sunday but now concern with this staining issue.

Any suggestions or recommendations

water Temp is 79

Plan was to put the inter cover on but leave everything running until temps drop. I do this to avoid the leave problem which is daily this time of year