Looking for some advice on a flat roof repair I’m planning to tackle myself.

I have a rubber (EPDM) flat roof with a molded pipe boot (IPS brand). The pipe/boot connection itself looks solid, but the rectangular base around it is about 70% loose and clearly delaminated.

The old mastic around the perimeter is dried, cracked, and lifting.This appears to be where water is getting in. I’ve been getting a mildew smell inside after rain.

Pipe is roughly 3–4" PVC. The boot base is about 15.5" x 12".

My goal is to:

Leave the pipe-to-boot connection alone (seems intact)

Address the perimeter where the boot meets the roof membrane.

I’m considering:

Cleaning and re-sealing the existing perimeter

Or doing an overlay repair with a larger EPDM patch over the whole area

I don’t have a big budget, so I’m trying to do this right without turning it into a bigger ordeal.

Questions:

Is an EPDM overlay patch the better long-term fix here vs just resealing?

Any issue leaving the existing boot in place and covering…