My master tree is on my PC in Family Historian. I upload the tree to various sites periodically as it grows and changes, by exporting to a Gedcom from FH and uploading to the sites. Yes, I create a new tree each time and delete the old one.
The only site I have problems with is My Heritage. I do currently have an account with them (they made me a too good to be true offer after not renewing for 6 months) but I have pretty much given up with amending or uploading new trees there. The last time I uploaded a new tree was a few years ago now. It is only in the last few weeks that their site seems to have synchronised with the "new" tree. I was still getting "Theory of Family Relativity" hints, but even after around 2 years, they were still based on my deleted tree and the hints showed "Deleted" against every individual on my side.
I tried to sort that out with MH support, but it was like banging my head against a brick wall.
A couple of months ago, I logged in to my MH account whilst I was temporarily in The Netherlands. I have been back home over a month now. A couple of weeks ago, they started sending me their regular emails about searches and hints, etc. in Dutch. Just had another one this morning.
But other than that, no real issues. I only upload my tree to the sites to take advantage of the search hints, DNA matches and Thrulines hints or similar. Hints get reset every time I upload a new tree, i.e. those I have previously viewed and which were no longer shown in my Ancestry tree, reappear when I upload a new tree. I can live with that, although a FH user has written a plugin to retain the hint history when uploading a new tree, but it's a fair amount of work to process the Gedcom through it, and I can't be bothered with the extra work because the results really don't bother me that much.